Spectrum Compact CE System TMD058

Spectrum Compact CE System
Operating Manual
Instructions for Use of Model Number CE1304
TMD058 | Revised 3/23

Table of Contents
1 Introduction.................................................................................................... 6
1.1 Spectrum Compact CE System Description ............................................... 6
1.2 Common Safety Precautions ......................................................................... 9
1.3 Safety Symbols and Marking ........................................................................10
1.4 Location of Instrument Safety Symbols on Oven Door ...........................11
1.5 Spectrum Compact CE System Specifications ........................................12
1.6 General Warnings ............................................................................................13
1.7 Product Components .....................................................................................14
1.8 Reagents and Consumables ........................................................................15
1.9 Laser Safety .....................................................................................................17
1.10 Environmental Requirements .......................................................................19
1.11 Unpacking, Installing and Moving
the Spectrum Compact CE System ............................................................19
1.12 Special Instructions ........................................................................................20
1.13 Electromagnetic Compatibility (EMC) Safety ............................................20
1.14 Chemical Safety ..............................................................................................21
1.15 Disposal of Waste Solution and/or Instrument ........................................21
1.16 Thermal Safety ................................................................................................22
1.17 Protection Against Computer Viruses ........................................................22
1.18 RoHS Marking for China ................................................................................23
2 Spectrum Compact CE System | TMD058 | Revised 3/23

2 Operating the System.................................................................................24
2.1 Turning On the Instrument ............................................................................24
2.2 Navigating the Spectrum Compact Software ..........................................26
2.3 Checking Consumable Status ......................................................................29
2.4 Preparing the Sample Cartridge ...................................................................31
2.5 Spectrum Compact CE System Workflow .................................................33
3 Managing Consumables............................................................................34
3.1 Maintenance Schedule for Consumables ..................................................34
3.2 Changing Consumables One at a Time ......................................................35
3.3 Uninstalling and Storing the Capillary Cartridge ......................................48
3.4 Installing All Consumables at One Time ....................................................51
4 Performing Calibrations.............................................................................52
4.1 Spatial Calibration ...........................................................................................52
4.2 Spectral Calibration ........................................................................................56
5 Performing a Run........................................................................................65
5.1 Preparing the Instrument ..............................................................................65
5.2 Preparing the Sample Cartridge ...................................................................65
5.3 Fragment Analysis ..........................................................................................66
5.4 Sequencing Analysis ......................................................................................78
5.5 Loading the Sample Cartridge ......................................................................86
5.6 Editing Injection Information Prior to Starting a Run ...............................88
5.7 Monitoring a Run ............................................................................................89
5.8 Exporting Results from Current Run ...........................................................99

6 Reviewing Completed Runs................................................................... 100
6.1 Reviewing Run Results ............................................................................... 100
6.2 Exporting Run Results ................................................................................ 102
6.3 Deleting Run Results ................................................................................... 103
6.4 Reviewing Log Information ........................................................................ 103
7 Managing Assays, Protocols and Dye Sets......................................... 108

7.1 General Settings and Protocol Security Symbols .................................. 109
7.2 Creating Protocols, Assays and Dye Sets ............................................... 111
7.3 Editing Protocols, Assays and Dye Sets .................................................. 134
7.4 Deleting Protocols, Assays and Dye Sets ................................................ 137
7.5 Exporting and Importing Protocols and Assays .................................... 137
8 Managing Instrument Settings.............................................................. 141

8.1 System Settings ........................................................................................... 142
8.2 Network Settings ......................................................................................... 143
8.3 Security Settings .......................................................................................... 144
8.4 User Accounts .............................................................................................. 147
8.5 Backup Settings ........................................................................................... 150
8.6 File Name Conventions ............................................................................... 151
8.7 Adjusting Date and Time ............................................................................ 156
9 Instrument Information........................................................................... 158

9.1 System Information ..................................................................................... 158
9.2 Alarm List ...................................................................................................... 159
10 Shutting Down the Instrument............................................................... 161

10.1 Short-Term Shutdown ................................................................................ 161
10.2 Long-Term Shutdown ................................................................................. 164

11 Error Messages......................................................................................... 165
12 Troubleshooting........................................................................................ 174
12.1 Instrument ..................................................................................................... 174
12.2 Spatial Calibration ........................................................................................ 176
12.3 Spectral Calibration ..................................................................................... 176
12.4 Sequencing Analysis ................................................................................... 179
12.5 Fragment Analysis ....................................................................................... 182
13 Protocol and Strip Setup Tools for Spectrum Compact .................. 185
13.1 Recommended System Requirements ................................................... 185
13.2 Spreadsheet Installation ............................................................................. 185
13.3 Protocol Setup Tool for Spectrum Compact ......................................... 188
13.4 Editing Existing Assays and Protocols .................................................... 189
13.5 Creating New Assays and Protocols ........................................................ 211
13.6 Deleting Assays and Protocols ................................................................. 213
13.7 Strip Setup Tool for Spectrum Compact ............................................... 213
14 Reviewing System Tests......................................................................... 225

14.1 Reviewing Fragment System Test Results ............................................. 226
14.2 Reviewing Sequencing System Test Results ......................................... 229
15 Summary of Changes.............................................................................. 232
All technical literature is available at: www.promega.com/protocols/

Visit the web site to verify that you are using the most current version of this Technical Manual.
E-mail Promega Technical Services if you have questions on use of this system: techserv@promega.com

Introduction 1
1.1 Spectrum Compact CE System Description
The Spectrum Compact CE System is an automated 4-capillary electrophoresis instrument
designed for a wide range of sequencing and fragment analysis applications. It is compatible
with existing fluorescently-labeled dideoxynucleotide triphosphate-based chain termination
sequencing chemistries along with 4-, 5- and 6-dye-labeled STR kits available from Promega
and other commercial vendors. Up to 32 samples may be run at a time.
The Spectrum Compact CE System is intended for:
Sanger Sequencing
• De novo sequencing
• NGS confirmation
• Resequencing
• Mutation detection
• Mitochondrial sequencing
Fragment Analysis
• Microsatellites
• PCR sizing
• STR genotyping
• SNP genotyping

Introduction
The instrument is controlled through a graphical user interface on a touch screen panel. An
external keyboard and mouse may also be used to control the software displayed on the touch
screen panel; these may be connected directly to the instrument via USB ports. The Spectrum
Compact Control Software provides a simple user interface with a clear display of useful
features including run setup, consumables and capillary cartridge usage information, and
system maintenance reminders. The Barcode Scanner is used to capture bar code information
on consumables for easy exchange and tracking of instrument consumables. The instrument
also offers the ability to monitor run progress and view results while analysis is in progress.
Exported files are compatible with commercially available data analysis software such as
GeneMarker®HID Software for Spectrum CE Systems, Mutation Surveyor®, GeneMapper®
version 4.1 or greater, and GeneMapper® ID-X.
Touch Screen Panel
Front Door Door Handle
Status Indicator
Power Switch
USB Port
for Storage
15763TA
Figure 1. Front of the Spectrum Compact CE System. Front view showing touch screen panel, front door,
status indicator and USB port. The power switch and door handle are located on the right side of the instrument.
Note: The Spectrum Compact CE System is not for medical diagnostic use.
Preloaded onto the Spectrum Compact CE System is the Spectrum Compact CE System
Remote Access Software. This software enables the user to create/edit/review/delete strip
IDs for sample strips, create/edit/review/delete protocols and assays, view analysis results,
monitor a Spectrum Compact CE System run in progress as well as completed runs, and
download completed runs using a web browser on a PC connected to the instrument either
directly or over a lab network. See the Spectrum Compact CE System Remote Access Software
#TMD064 for instructions for use.

Introduction
Air Intake Panel
USB Keyboard USB Bar Code

Connection Connection
Air
Exhaust
Panel
Power
Connection
15764TA
Ethernet Connection
Figure 2. Rear of the Spectrum Compact CE System. The back of the Spectrum Compact CE System has an
air intake panel, air exhaust panel, power connection, USB keyboard connection, USB barcode connection
and Ethernet connection.
Notes:
1. Never use password-protected USB drives. If a USB drive is password protected, the
USB icon may still become active upon connecting to the instrument, but when export is
executed, the export will fail.
2. Do not perform keyboard operations and do not attach or remove the keyboard or barcode
scanner while accessing the USB device. This may result in failure.
3. Do not connect cables other than a LAN cable to the Ethernet port. This may result in failure.
Detection Oven Door

Window
Capillary
Cartridge Sample
Cartridge
Anode
Buffer
Cartridge Cathode
Buffer
Cartridge
Polymer
Cartridge
and Polymer Autosampler
Delivery
Unit (PDU)
15765TA
Figure 3. Interior of the Spectrum Compact CE System. The interior of the system provides access to key
components. Instructions for maintaining the buffer, polymer and capillary cartridges are provided in Section 3,
Managing Consumables.

Introduction
Component Function
Oven Maintains temperature around the capillary array during
electrophoresis.
Capillary Cartridge Contains the array of 4 capillaries (36cm), which enables
electrophoretic separation of fluorescently labeled DNA
fragments.
Detection Window Area where fluorescence is detected.
Anode Buffer Cartridge (ABC) Contains running buffer for electrophoresis.
Cathode Buffer Cartridge (CBC) Contains running buffer for electrophoresis.
Sample Cartridge Holds up to 4 × 8-well strip tubes containing samples.
Polymer Cartridge Contains either Spectrum Compact Polymer4 or
Spectrum Compact Polymer7, which is pumped via the
Polymer Delivery Unit into the capillary cartridge for
separation of fragments.
Autosampler Houses the Sample Cartridge, ABC, CBC and Polymer
Cartridge. Adjusts their position relative to the capillary
cartridge during run cycles for proper injection and washes.
Polymer Delivery Unit (PDU) Actuates plunger in Polymer Cartridge to deliver polymer
to the capillary cartridge.
1.2 Common Safety Precautions

• Follow all precautions labeled on the instrument and described in this manual.
• Do not use this instrument for anything other than its designed purpose.
• Do not perform any operations and maintenance other than those described in this manual.
• Only perform the maintenance activities described in the manual. Contact Technical Service
for further maintenance and repair.
• Preventive Maintenance, provided by Promega service, is strongly recommended to ensure the
safety and performance of the instrument. Contact Technical Service for further information.
• Never modify the instrument.
• Do not use any parts that are not specified by Promega.
• Customers should not attempt the initial unpacking upon delivery or relocation of the
instrument.
• Keep in mind that the hazard warnings in the manuals or on the product cannot cover every
possible case, as it is impossible to predict and evaluate all circumstances beforehand.
Always be alert and use common sense.
• The guidance provided in this manual is intended to supplement, not supersede, the normal
safety requirements prevailing in the user’s country.

Introduction
1.3 Safety Symbols and Marking
Safety Symbols and Markings

Warning. Risk of personal injury to the operator or a safety hazard to the
instrument or surrounding area.
Danger. Hazardous voltage. Risk of electric shock.
6687TA.eps
Warning. Hot surface. Burn hazard.
Warning. Sharp objects inside.
This label indicates laser radiation is present.
SYMBOLS KEY
Symbols Explanation Symbols Explanation

Catalog Number Lot Number
Serial Number Manufacturer

11332TA
Date of Manufacture Consult your local Promega

(Year-Month-Day) Representative regarding
instrument disposal
WEEE Directive (European
Community Directive
2012/19/EU on Waste
Electrical and Electronic
6687TA.eps
Equipment)

Introduction
1.4 Location of Instrument Safety Symbols on Oven Door
16411TA
Danger! Hazardous voltage. Risk of electric shock.
Do not remove instrument panels. Do not touch internal parts or circuits while the instrument
power is turned on. This may cause death or serious injury due to electric shock.

Introduction
1.5 Spectrum Compact CE System Specifications
Processing Time 30–60 minutes, depending on application

Number of Samples Up to 32 samples (4 × 8-well strip tubes) per run
Weight 45kg (99lb)
Dimensions (W × D × H) 15.75 × 23.62 × 23.62 inches (400 × 600 × 600mm)
Power Requirements 100-240Vac, 50/60Hz, 260VA
Overvoltage Category II
Pollution Degree 2
Ground Grounding resistance 100Ω or less
Leave at least 7.9 inches (200mm) at the right side of the instrument so that the power supply
switch is easily accessible and 15.8 inches (400mm) at the left side to allow clearance for
opening the instrument door. At least 3.9 inches (100mm) should be left at the back of the
instrument to allow for easy connection/disconnection of power cable and USB connections at
the rear of the instrument.
이 기기는 업무용 환경에서 사용할 목적으로 적합성평가를 받은 기기로서 가정용 환경에서

사용하는 경우 전파간섭의 우려가 있습니다.
This device has been evaluated for conformity for use in a business environment, and if used in
a home environment, there is a risk of radio interference.
Important! Power connectors
The Spectrum Compact CE System is delivered with a detachable power cord that meets
the power requirements listed above. In areas where the supplied power is subject to voltage
fluctuations exceeding ±10% of the nominal value, a power line regulator may be required. High
or low voltages can adversely affect the electronic components of the instrument.
We recommend the use of an uninterruptible power source (UPS) for the Spectrum Compact
CE System. At a minimum, the instrument should be connected through a surge suppressor.
Danger! Hazardous voltage. Risk of electric shock.
Use properly configured and approved line cords for the voltage supply in your facility as
specified by Promega. Incorrect connection of the power cord could result in fire or electrical
shock.
Place instrument in a location so that the power cord is accessible and can be easily
connected and disconnected.

Introduction
Warning! Sharp objects inside.
The electrode-end and capillary head-end of the capillary cartridge can lead to piercing injury.
To avoid injury, do not touch the tip of the capillary cartridge.
Warning! Sharp objects inside.
The tip of the anode electrode can lead to piercing injury. To avoid injury, do not touch the tip of
the anode electrode.
Warning! Physical injury hazard
Do not touch moving parts while operating the instrument. Disconnect power before
performing maintenance on the instrument.
1.6 General Warnings
Handling
• Avoid pressing on the display monitor with excessive force. Otherwise, a malfunction may
result.
• If there are contaminants such as fingerprints or water droplets on the display monitor, wipe
them off lightly with a soft and dry cloth, or a soft damp cloth.
• The display monitor is made of glass. If the display monitor is broken, avoid direct contact
with the shards of the glass. Otherwise, injury may result.
• The touch panel monitor may become inoperable after approximately 5 million touches at
the same spot.
Touchscreen
• Depending on the type of image displayed, bright pixels (pixels that are lit regardless of the
specified color) or black pixels (pixels that do not represent the specified color) may be
visible on the screen, or part of ruling lines or characters may appear missing.
• Missing pixels or constantly lit pixels on the liquid crystal display screen do not indicate an
instrument malfunction.

Introduction
• Depending on the image displayed, the screen may appear to flicker. Adjust your viewing
angle to the screen to improve view.
• If the same image is displayed on the screen for a long time, a remnant of this image may
remain even after the screen has changed. This will eventually fade and disappear.
• The temperature of the liquid crystal may rise after long and continuous use. This may lead
to changes, irregularities or both in contrast. These effects will subside as the temperature
falls.
• The screen may appear dark when the instrument is first turned on. Brightness will increase
as time passes.
• Due to the multicolor imaging elements and the liquid crystal structure, the display on the
screen may be difficult to view from an upward angle. Adjust your viewing angle to the
screen to improve view.
• Small air bubbles or ring-shaped stripe patterns may be visible on the display monitor
screen. They do not affect the operation of the instrument.
Handling the instrument and peripheral devices

• Promega Corporation is not responsible for any loss or damage done to data or applications
due to broken hardware.
• Static electricity has an adverse effect on the instrument and peripheral devices. Avoid
using materials which can generate static electricity when operating the instrument, such as
walking on a carpet or wearing a lap blanket.
1.7 Product Components

P R O D U C T C A T. #
Spectrum Compact CE System CE1304
Includes:
• Spectrum Compact CE System

• Spectrum Compact Control Software
• Spectrum Compact CE System Remote Access Software
• Spectrum Compact CE System Standard 1-Year Warranty

Introduction
1.8 Reagents and Consumables

Storage and
Consumable Cat.# Handling On-Instrument Storage
Spectrum Compact Buffer CE2300 +2°C to +10°C 14 days, 80 injections or expiry date
(Environmental temperature: 25°C or less)
Spectrum Compact Polymer4 CE2304 +2°C to +10°C 14 days, 16 injections or expiry date
Compatible with all Spectrum Compact
software versions.
Compatible only with Spectrum Compact
software version 6138200-## and later.*
Compatible with all Spectrum Compact
software versions.
Compatible only with Spectrum Compact
software versions 6138200-## and later.*
Spectrum Compact Cathode Septa Mat CE2301 +15°C to +30°C One-time use per CBC
Spectrum Compact Cathode Retainer CE2302 +15°C to +30°C NA
Spectrum Compact Strip Base & Retainer,
CE2332 +15°C to +30°C NA
32-Well
Strip Septa Mat, 8-Well CE2308 +15°C to +30°C One-time use per sample
Capillary Preservation Buffer CE2399 +2°C to +10°C NA; expiry date
Spectrum Compact Capillary Cartridge, 300 injections or expiry date
4-Capillary 36cm Note: Spectrum Compact software
CE2340 +15°C to +30°C versions below 6138200-## will show a
200 injection limit but it can be used for
300 injections.
NA = not applicable
Not for Medical Diagnostic Use.
*Not compatible with Spectrum Compact software versions 6138000-## and earlier.

Introduction
Additional supplies and consumables are necessary for routine operation of the Spectrum Compact
CE System. Contact Promega to order these additional supplies.
Important! Only use parts and devices specified by Promega Corporation
Gripping
Knob
Capillary
Cover
Detection
Window
Capillaries
Anode
Cathode
15766TA
Figure 4. Spectrum Compact Capillary Cartridge, 4-Capillary 36cm. The interior is shown on the left and the
exterior on the right. Protective caps on anode and cathode end of array are shown. These may be filled with
Capillary Preservation Buffer for long-term storage of used capillary cartridges.
Cathode
Retainer
Film
Cathode
Septa Mat
Container
15767TA
Figure 5. Spectrum Compact Buffer Cartridges. The anode buffer cartridge (ABC) is shown on the left and
the cathode buffer cartridge (CBC) with septa mat and retainer on the right. A clear protective seal must
be peeled off the top of the CBC prior to placing the Spectrum Compact Cathode Septa Mat and Retainer onto the
CBC. Do not remove the white seal from the top of the ABC.

Introduction
Foil Seal
Skirt
Plunger
15768TA
Syringe Barrel
Figure 6. Spectrum Compact Polymer Cartridge. The foil seal must be peeled off the top of the Spectrum
Compact Polymer Cartridge prior to placing it into the polymer delivery unit on the autosampler of the
Spectrum Compact CE System.
1.9 Laser Safety

Spectrum Compact complies with 21 CFR 1040.10 and 1040.11. Class 1 Laser Product.
The laser specifications are:
• Wavelength: 505nm
• Output power: 20mW
To ensure safe laser operation:
• Do not remove the instrument protective panels or safety labels.

• Do not disable safety interlocks.
• Never look directly into the laser beam.
• Remove reflective objects such as jewelry and wristwatches.
• Wear proper eye protection and post a laser warning sign at the entrance to the laboratory if
panels are removed for service.
Warning! This label indicates laser radiation is present.
Class 3B laser radiation when open and interlocks defeated. Avoid exposure to the beam.

Introduction
Use of controls or adjustments or performance of procedures other than those specified herein
may result in hazardous radiation exposure.
The Barcode Scanner (Cat.# CE5300) that is used with the instrument to capture bar code
information for samples and reagents is categorized as a Class 2 laser product. Class 2 lasers
are low-power, visible-light lasers that can damage the eyes. Never look directly into the laser
beam. The scanner is designed to prevent human access to harmful levels of laser light during
normal operation, user maintenance or prescribed service operations.
Class 2 lasers can cause damage to eyes. Avoid looking into a Class 2 laser beam or pointing a
Class 2 laser beam into another person’s eyes.
Use of controls or adjustments or performance of procedures other than those specified herein
may result in hazardous radiation exposure.

Introduction
1.10 Environmental Requirements
Power Requirements 100-240Vac, 50/60Hz, 260VA

Temperature During Transportation and –20°C to 60°C
Storage
Temperature During Operation 15°C to 30°C with changes <±2°C/hour
Humidity During Transportation and Storage 20% to 80%RH
Humidity During Operation 20% to 80%RH
Operating Altitude <2,000m
Pollution Degree 2
The Spectrum Compact CE System is intended for indoor use only. To avoid shortening the
expected lifespan of the instrument, the Spectrum Compact CE System must be installed in a
location that meets the following criteria:
• Use a sturdy, level surface (no perceptible vibration).

• Avoid dusty areas.
• Choose a location that has good air circulation and is not exposed to direct sunlight.
• Use an uninterruptable power source (UPS) rated to support the power requirements above.
Contact a Promega representative for a recommended UPS.
• Do not install in a location with large temperature variability or high humidity.
• Do not position the instrument so that it is difficult to unplug from the power source.
• Do not place next to heating or cooling sources.
• Do not use near flammable gases or liquids.
• Do not place near other electrically sensitive instruments.
• Do not use extension cords. Relocate the instrument, power receptacle and/or UPS to avoid
using an extension cord.
1.11 Unpacking, Installing and Moving the Spectrum Compact CE

System
A Promega representative must perform unpacking, installing and moving of the Spectrum
Compact CE System. Performance of any of these activities by noncertified individuals may
invalidate the product warranty or service contract terms.

Introduction
1.12 Special Instructions

• Wipe up spills immediately.
• The Spectrum Compact CE System contains sensitive optical components and precision-
aligned mechanical assemblies. Handle with care.
• Use caution when working with solvents, as they may damage the plastic case of the
• Do not expose the Spectrum Compact CE System to temperatures outside the specified
range (see Section 1.10), because damage to the unit may occur that will not be covered
under warranty.
• Changes or modifications to the instrument not expressly approved by Promega could void
the warranty.
• Do not use this Spectrum Compact CE System for anything other than its intended use.
• Always disconnect the power before cleaning or performing routine instrument
maintenance.
• Do not disassemble the Spectrum Compact CE System other than as specified in this
operating manual for routine instrument maintenance and use.
• If the equipment is used in a manner other than that specified by Promega, the protection
provided by the equipment may be impaired.
• Do not overfill strip wells, because this may lead to spills and/or instrument damage.
1.13 Electromagnetic Compatibility (EMC) Safety

Spectrum Compact CE System complies with the emission and immunity requirements
prescribed by EMC standard IEC 61326-1:2012 (Group 1, class A, Basic environment).
If installed adjacent to other electrical and electronic equipment, they may adversely affect
each other. Equipment operation and measurement results may be affected by noise from
peripheral devices. Alternatively, noise from the device may affect the operation of peripheral
devices and measurement results.

Introduction
1.14 Chemical Safety

Caution! Chemical hazard
Formamide may be combustible at high temperature, and slightly flammable in presence of

heat, sparks or open flames. Keep away from heat or sources of ignition. Refer to the Safety
Data Sheet (SDS) provided by the manufacturer to handle the reagent.
Formamide is an irritant and a teratogen; avoid inhalation and contact with skin. Read the
warning label, and take appropriate precautions when handling this substance. Always wear
gloves and safety glasses when working with formamide.
Before handling any chemicals, refer to the Safety Data Sheet (SDS) provided by the
manufacturer and observe all relevant precautions in handling each chemical.
All chemicals in the instrument, including liquid in the lines, are potentially hazardous. Always
determine what chemicals have been used in the instrument before changing reagents or
instrument components. Wear appropriate protective equipment (e.g., protective clothing,
gloves) when working on the instrument.
1.15 Disposal of Waste Solution and/or Instrument

• To dispose of the instrument, follow the local environmental protection regulations.
• Do not dispose of this instrument as unsorted municipal waste. Follow local municipal
waste ordinances for proper disposal provisions to reduce the environmental impact of
waste electrical and electronic equipment (WEEE). For European Union customers, Contact
Promega Service for equipment pick-up and recycling.
• To dispose of waste solutions, read and understand the Safety Data Sheets (SDSs) provided
by the manufacturers of the chemicals in the waste container.
• This instrument is equipped with a touch panel PC, which contains a lithium battery.
• Prior to instrument disposal, ensure that any important data has been archived.

Introduction
1.16 Thermal Safety

Warning! Hot surface. Burn hazard.
The inside surface of the oven can reach a temperature of 70°C. Ensure that the oven is off
before replacing the capillary cartridge. When replacing the capillary cartridge, grasp the yellow
handle of the cartridge and do not touch the inside surface of the oven.
Warning! Hot surface. Burn hazard.
The oven remains hot after the instrument stops.
1.17 Protection Against Computer Viruses

The Spectrum Compact CE System comes installed with McAfee application control software
(whitelist) as anti-virus software. Application “whitelisting” is the practice of specifying an index
of approved software applications that are permitted to be present and active on a computer
system. McAfee application control software will allow only those programs that are on the
“whitelist” (i.e., approved list) of applications to run. No other applications will be allowed to
run on the instrument panel PC. Thus there is no need for updates, since only the Spectrum
Compact CE System applications will be on the approved list. If despite whitelisting the
instrument becomes infected with a virus, contact Promega Technical Services.

Introduction
1.18 RoHS Marking for China

Names and contents of hazardous substances contained in products.
有害物质
部件名称铅汞镉六价铬多溴联苯多溴二苯醚
（Pb）（Hg）（Cd）（Cr（Ⅵ））（PBB）（PBDE）
照射单元 × ○ ○ ○ ○ ○
检测单元 × ○ ○ ○ ○ ○
自动进样器 × ○ ○ ○ ○ ○
恒温组件 × ○ ○ ○ ○ ○
高压电源组件 × ○ ○ ○ ○ ○
线路板 × ○ ○ ○ ○ ○
架台 × ○ ○ ○ ○ ○
成套附属品 × ○ ○ ○ ○ ○
本表格依据SJ/T 11364的规定编制。
○：表示该有害物质在该部件所有均质材料中的含量均在GB/T 26572规定的限量要求以下。
×：表示该有害物质至少在该部件的某一均质材料中的含量超出GB/T 26572规定的限量要求。
SYMBOLS KEY
Symbols Explanation
RoHS Marking for China indication Environment
Friendly Use Period of 10 years.

Operating the System 2
2.1 Turning On the Instrument
1. Confirm that the instrument is connected to an appropriate uninterruptible power supply
(UPS) and is on a protected circuit.
2. Verify that the Instrument Door is closed.
3. Turn on the instrument by turning the power switch on the right side of the instrument to
the up position.
4. Software launches automatically. During this time the status indicator flashes amber. After
the software has successfully launched the status indicator changes to a steady green (no
flashing).
5. Log in to the software by selecting the appropriate user name from the drop-down menu
and entering the correct password (Figure 8).
Notes:
1. When the instrument is set with the normal security level (see Section 8.3), the login
screen will be skipped. The main menu is displayed after the startup screen is closed.
2. If you want to change the password, select Change Password. Enter a new password
in the New Password and Re-enter New Password boxes on the Change Password
screen.
3. The window in Figure 7 may be displayed when the instrument is powered up after a
new device (USB memory, keyboard, barcode scanner, etc.) is connected. If displayed,
select the X on the window to close it. The instrument can then be used normally.
16647TA
Figure 7. Spectrum Compact CE System Software New Device window.

Operating the System
15769TA
Figure 8. Spectrum Compact CE System Software Login screen.
The instrument status indicator indicates six states:
State Status
No light Instrument is off
Flashing amber light Instrument is initializing, door is open, or run failure
Steady green light Power is on and in standby
Flashing green light Power is on and instrument is in use (calibration, electrophoresis,
etc.)
Flashing red light Failed initialization or a critical error has occurred
Steady amber light Instrument was shut down incorrectly
Important!
If the software stalls, power OFF the instrument using the power switch at the right side and
restart the instrument.

2.2 Navigating the Spectrum Compact Software

Upon launching and logging into the Spectrum Compact Control Software, the ‘Main Menu’
screen will be displayed (Figure 9). The ‘Main Menu’ screen provides access to the four
workflow menus (Run, Review, Maintenance and Protocols) as well as status indicators. The
screen is divided into three sections: Header, Main Menus and Footer.
Header
Main
Menus
15770TA
Footer
Figure 9. Spectrum Compact CE System Software Main Menu screen. The Header and Footer are fixed and
remain available to the user across all menu screens. The navigation and informational icons displayed
in these areas will vary depending on the specific workflow menu as well as selected security level.
Within specific workflow menus, a navigation bar below the header will indicate the user’s
current location within the Spectrum Compact Control Software. In the example below
(Figure 10), the navigation bar indicates the user has navigated to the ‘Run List’ screen within
the Completed Runs screen.
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Figure 10. Spectrum Compact CE System Software ‘Run List’ bar.
The Spectrum Compact Control Software contains several navigation and informational icons
in the header. Each icon provides information about a specific function or component.
Note: The Screen Lock icon (see table below) in the header is only available under High
Security level settings (see Section 8.3).
Icon Type Function

Displayed when an alarm has been triggered. This indicator
Alarm also acts as a shortcut icon to the ‘Alarm List’ screen, which
shows details of the alarm (see Section 9.2).
Select this icon to open the ‘Consumables’ screen, which
shows detailed information of each installed consumable
Consumables and which consumables may need to be replaced. This icon
will display a consumable status indicator (see Section 2.3)
if any consumables need replacement.

Icon Type Function

Selecting this icon moves the autosampler forward to allow
Eject access to consumables and the sample cartridge.
Displayed when a USB drive is connected to the instrument.

USB Select the USB icon to safely remove the USB drive from the
instrument.
Locks the operation panel. To unlock, enter the appropriate
user name and password.
Note: This function is only available under High Security
Screen Lock
level settings (see Section 8.3). When the screen is locked,
only an administrator or user can unlock the screen using
their login password.
Displays the oven temperature. Select the Oven
Temperature icon to turn on the oven. The icon flashes
while oven is heating up to 60°C.
Notes:
1. Selecting the Oven Temperature icon only allows
Oven
preheating to 60°C. No other oven temperature can be set
Temperature
on this screen.
2. Selecting this icon when the oven is at 60°C temperature
does not turn off the oven.
3. If samples are not run, the oven unit will turn off after
2 hours.
Displayed when remote access user is logged on via the
Network network. Select the Network Access icon to view the
Access ‘Network Access Users’ screen that displays the ID of the user
logged on remotely to the Spectrum Compact CE System.
Displays the instrument status.
Standby: System is idle but ready to start a run.
Run: Injection is in process.
Stop: Instrument is in the process of stopping but is not idle
Instrument (this is not the same as when the instrument stops due to
Status an error).
Open: Front door or oven door is open.
Recovery: Initialization after closing door.
Error: An error is detected and the run has stopped.
Critical: Instrument trouble.
Date & Time, Displays the current date (month, day, year), time (12-hour
Login User clock format) and login user name.
Name
Note: Connecting some USB devices to the Spectrum Compact CE System may not activate
the USB icon. In that case, remove the USB device without touching the USB icon.

The icons displayed in the footer provide several software shortcuts.
Icon Name Function

Logs out the current user.
Log out Note: This function is only available under High Security level
settings (see Section 10). Displayed only on the ‘Main Menu’
screen under High Security level settings.
Shuts down the instrument.
Note: Displayed only on the ‘Login’ screen after logging out of
Shutdown the ‘Main Menu’ screen under High Security level settings, or
on the ‘Main Menu’ screen under Normal Security level settings
(see Section 10).
Shortcut to Main Screen.
Home
Displays the following sub menu (see Section 9):

• About
About
Displays the following sub menus (see Section 8):

• System Settings
• Network Settings
• Security Settings
Settings • User Rights1
• User Accounts
• Backup Settings
• File Name Convention
• Service2
1
The ‘User Rights’ screen is only accessible via User Rights on the ‘Security Settings’ screen (Section 8.3).
2
When security level is set to Normal (Section 8.3), an additional button is visible on the ‘Settings’ screen called
Service. This setting is for use by Promega service engineers.

2.3 Checking Consumable Status

Before starting a run on the Spectrum Compact CE System, ensure all consumables are
installed and in sufficient supply. For best quality results, use unexpired reagents that are
within the recommended use range (see Section 1.5). Refer to the ‘Consumables’ screen to
determine if any consumables need to be replaced (Figure 11). To access the ‘Consumables’
screen, select Consumables in the Header.
The ‘Consumables’ screen displays information for the four consumables on the instrument:
Polymer, Capillary Cartridge, and Anode and Cathode Buffers.
Status
Indicator
Type
Usage Count
(Injections)
Expiration
15771TA
Date
Figure 11. Spectrum Compact CE System Consumables screen. Usage count (number of injections), on-
instrument expiration date and remaining injections are displayed on the ‘Consumables’ screen for each
consumable as well as polymer type.
Note: Either a 16- or 24-injection polymer cartridge may be used with Spectrum Compact
software version 6138200-## and later, but only a 16-injection cartridge may be used with
Spectrum Compact software versions below 6138200-##. Installing a 24-injection polymer
cartridge on software versions below 6138200-## will result in the following warning: “Cannot
identify consumable. Read appropriate consumable bar code.”
A consumable status indicator will appear on the icons of consumables that need attention.
There are three indicators:
Symbol Description
Reaching consumable expiration date, on-instrument
expiration date or injection limit for consumable.
Consumable expiration date, on-instrument

expiration date or injection limit for conumable
has passed.
Cannot perform a run because the maximum
injection count was reached for the polymer.

The following information can be accessed by touching the icon for each specific consumable:
• Type of consumable
• Material number
• Lot number
• Serial number
• Expiration date
• Initial installation date
• On-instrument expiration date
• Injection count
The expiration date, injection count maximum and on-instrument expiration date correspond
to the recommended usage for each installed consumable. The status indicators will adjust to
indicate when a consumable is reaching its expiration date, on-instrument expiration date or
when it is past these dates, as well as when the recommended number of injections has been
exceeded.
The only hard stop for the system is for the polymer. The software will not allow a run to
proceed if the scheduled number of injections exceeds the remaining injections of the polymer,
because this would damage the system. All other consumable warnings are advisory in nature
and will not stop a run.
Consumables can be replaced individually or all at once. To replace an individual consumable,

select the icon for the specific consumable. This will display the ‘Installed Consumable
Information’ screen for the consumable (Figure 12). Selecting Install on this screen will launch
the replacement wizard (see Section 3).
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Figure 12. Spectrum Compact CE System ‘Installed Consumable Information’ screen.

2.4 Preparing the Sample Cartridge

Samples prepared in 8-well strip tubes are assembled into the strip base and retainer (Figure
13) to form the sample cartridge (Figure 14), which can be loaded onto the Spectrum Compact
CE System. Samples are injected in groups of four, such that one 8-well strip tube can be used
for two injections. Each 8-well strip tube corresponds to one lane (A, B, C or D) of the sample
cartridge. Samples are injected in groups of four across a lane (not by column). For example,
samples in well positions A1 through A4 in lane A are injected together, followed by samples in
well positions A5 through A8 for the second injection. This pattern is then repeated for samples
in lanes B, C and D. You can change the order of injections during run setup (see Section 5.6).
Notes:
1. Only use MicroAmp™ Optical 8-Tube Strips (0.2ml) (Applied Biosystems® Cat.# 4316567)
as a source of 8-well strip tubes. Use of other 8-well strip tubes may affect performance or
damage the Spectrum Compact CE System.
2. Wear gloves when handling consumables and sample cartridges.
Wells
1 2 3 4 5 6 7 8
A Injection 1 Injection 2
B Injection 3 Injection 4
Lane
C Injection 5 Injection 6
D Injection 7 Injection 8
To prepare the sample strip(s) for placement onto the instrument:
1. Place a Strip Septa Mat, 8-Well, over the wells of each 8-well strip tube containing the
sample loading cocktail. Refer to the technical manual of the sequencing or fragment
analysis kit for how to prepare the sample loading cocktail.
Notes:
1. Be sure the samples are positioned at the bottom of each well and are free of bubbles.
Briefly centrifuge the sample 8-well strip tube(s) if needed.
2. To prevent cross-contamination, do not reuse Strip Septa Mat, 8-Well. Always use a
new Strip Septa Mat, 8-Well, for each 8-well strip tube.
2. Place the 8-well strip tube(s) with Strip Septa Mat, 8-Well into the strip base. When using
less than four strips in the run, you can place the strips in any lane.
Note: Lane names A to D and well numbers 1 to 8 are embossed on the strip base. Be sure
to check the lane name when placing a sample 8-well strip tube into the strip base to make
certain that the correct 8-well strip tube is in the correct lane.
Additionally, well numbers 1 to 8 are embossed on each 8-well strip tube. When placing a
sample 8-well strip tube into the strip base, be sure that the well numbers on each sample
8-well strip tube match those on the strip base.

3. To complete the strip assembly, place the retainer over the strip(s) in the strip base,
aligning the lane names A to D and well numbers 1 to 8 on the retainer to those on the strip
base and pressing until the retainer clicks into the strip base.
Strip Base Retainer
Cutout
Faces Handle
Front
Strip Septa
8-Well Mat
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Strip Tube
Figure 13. Assembling the Spectrum Compact Strip Base and Retainer.
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Figure 14. Assembled Spectrum Compact Sample Cartridge.

2.5 Spectrum Compact CE System Workflow

Operational workflow is shown with corresponding sections of the Spectrum Compact CE
System Manual as reference for more detailed information.
Turn on instrument. • Turning On the Instrument: Section 2.1
Check consumables status.

Replace consumables • Checking Consumable Status: Section 2.3
if necessary. • Managing Consumables: Section 3
Check calibrations.
Run new if necessary.
• Performing Calibrations: Section 4
Prepare sample cartridge. • Preparing the Sample Cartridge: Section 2.4
• Fragment Analysis: Section 5.3

Assign strip information.
• Sequencing Analysis: Section 5.4
• Loading the Sample Cartridge: Section 5.5

Loading the sample • Editing Injection Information Prior to
cartridge and starting a run.
Starting a Run: Section 5.6
Monitoring run, reviewing • Monitoring a Run: Section 5.7

and downloading results. • Reviewing Runs: Section 6
If new protocols or assays are required to

run samples, perform the following before preparing
samples and assigning strip information.
Create new protocols/assays

or edit existing • Managing Assays and Protocols: Section 7
protocols/assays.
Proceed to prepare
16067MA
sample cartridge.

Managing Consumables 3
Managing consumables is done through Consumables in the header. Selecting Consumables
displays the ‘Consumables’ screen (Figure 11), which shows the current status of the four
consumables: Spectrum Compact Polymer (4 or 7), Spectrum Compact Capillary Cartridge,
Spectrum Compact Anode Buffer Cartridge (ABC) and Spectrum Compact Cathode Buffer
Cartridge (CBC) (see Section 2.3).
3.1 Maintenance Schedule for Consumables

Consumable Cat.# On-Instrument Storage
Spectrum Compact Buffer CE2300 Once seal is pierced (anode) or removed (cathode), the anode
and cathode buffers are stable for 14 days, 80 injections or
until expiry date, whichever comes first.
Spectrum Compact Polymer4 CE2304 14 days, 16 injections (64 wells) or until expiry date, whichever
comes first. Compatible with all Spectrum Compact software
versions.
comes first. Compatible only with Spectrum Compact
software versions 6138200-## and later.1
comes first. Compatible with all Spectrum Compact software
versions.
comes first. Compatible only with Spectrum Compact
software versions 6138200-## and later.1
Spectrum Compact Capillary Cartridge, CE2340 300 injections or expiry date, whichever comes first.2
4-Capillary 36cm
Consumables can be replaced individually, as needed, or all at once. Instructions are provided below for changing consumables one at a time
and all at the same time.
1
Not compatible with Spectrum Compact software versions 6138000-## and earlier.
2
The injection limit for CE2340 will display as 200 injections on Spectrum Compact software versions 6138000-## and earlier, but it can be
used for 300 injections.

Managing Consumables
Notes:
1. The ABC and CBC should be replaced at the same time.
2.
Do not install consumables on one Spectrum Compact CE System that have been
previously installed on another instrument, as information about the previous usage will
not transfer to the new Spectrum Compact CE System.
3.2 Changing Consumables One at a Time
Installing the Anode Buffer

Change the anode buffer every 14 days or 80 injections to ensure optimal results. The anode
buffer cartridge should be equilibrated to room temperature before installing on the Spectrum
Compact CE System.
1. Clean the surface of the film with a lint-free tissue.
Important!
Do not peel the film off the cartridge.
2. Select Anode Buffer on the ‘Consumables’ screen (Figure 11). This will open the ‘Installed
Anode Cartridge Information’ screen (Figure 15). 15775TA
Figure 15. ‘Installed Anode Cartridge Information’ screen.
3. Select Install in the footer to start the replacement wizard. This will open the ‘Anode
Cartridge Barcode Scanning’ screen (Figure 16).

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Figure 16. Anode cartridge barcode scanning screen.
4. Use the Barcode Scanner connected to the Spectrum CE Compact System to read the
barcode label on the Spectrum Compact ABC. Information about the Spectrum Compact
ABC being installed is displayed on the ‘Anode Cartridge Information’ screen (Figure 17).
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Figure 17. ‘Anode Cartridge Information’ screen.
5. Check the information displayed (e.g., confirm that the Spectrum Compact ABC is within
its expiry date) and select Next on the lower right of the footer. Autosampler moves to front
of instrument and status indicator flashes green. Do not open the instrument front door
when status indicator flashes green. After autosampler has stopped moving, status
indicator turns steady green and the ‘Install the Cartridge’ screen appears.
6. When the ‘Install the Anode Buffer Cartridge’ screen appears (Figure 18), open the front
door of the instrument.

15778TA
Figure 18. ‘Install the Anode Buffer Cartridge’ screen.
7. Remove the old Spectrum Compact ABC (if present) by pressing in on the clear locking
tabs on either side of the old Spectrum Compact ABC and pulling up to detach it from the
deck.
8. Mount the Spectrum Compact ABC on the deck by aligning the two holes on the bottom of
the cartridge to the two circular posts protruding from the deck.
Note: The holes and the posts are of two sizes (large and small diameter), such that the
cartridge can only be inserted in one orientation.
9. Push the cartridge down until an audible click is heard and the cartridge is secured in
place.
10. Close the front door and wait for the status indicator to stop flashing amber and turn
steady green.
11. Select Next on the lower right of the footer of the ‘Install the Anode Buffer Cartridge’
screen.
12. Select Finish on the ‘Installation Completed’ screen (Figure 19).
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Figure 19. ‘Installation Completed’ screen.

Note: Until Finish is selected, the ‘Installed Anode Cartridge Information’ screen consumables
status indicator (see Section 2.3) will continue to display the status of the old consumable.
Installing the Cathode Buffer

Change the cathode buffer every 14 days or 80 injections to ensure optimal results. The
cathode buffer cartridge should be equilibrated to room temperature before installing on the
1. Peel the seal from the top of the Spectrum Compact CBC.
2. Press the Spectrum Compact Cathode Septa Mat into the holes in the top of the Spectrum
Compact CBC.
Note: Use a new Spectrum Compact Cathode Septa Mat each time you install a new
Spectrum Compact CBC.
3. Attach the retainer on top of the septa, making sure that the heads of the septa protrude
through the holes in the retainer. Make certain that clips on the side of the retainer are fully
engaged under the lip at the top of the Spectrum Compact CBC (Figure 20).
Notes:
1. Replace ABC and CBC at the same time.
2. To prevent contamination, do not reuse the CBC septa. Use a new CBC septa.
Cathode Retainer
Cathode
Septa Mat
Retainer Clips Engaged

Under Lip of Cartridge
Spectrum Compact CBC

15780TA
Figure 20. Assembled Spectrum Compact CBC.

4. Select Cathode Buffer on the ‘Consumables’ screen (Figure 11). This will open the
‘Installed Cathode Cartridge Information’ screen (Figure 21).
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Figure 21. ‘Installed Cathode Cartridge Information’ screen.
5. Select Install in the footer to start the replacement wizard. This displays the ‘Cathode
15782TA
Figure 22. ‘Cathode Buffer Cartridge barcode scanning’ screen.
6. Use the Barcode Scanner connected to the Spectrum CE Compact System to read the
barcode label on the Spectrum Compact CBC. After reading the bar code, information
about the Spectrum Compact CBC being installed is displayed on the ‘Cathode Cartridge
Information’ screen (Figure 23).

15783TA
Figure 23. ‘Cathode Cartridge Information’ screen.
7. Check the information displayed (e.g., confirm that the Spectrum Compact CBC is within
its expiry date) and select Next on the lower right of the footer. Autosampler moves to front
of instrument and status indicator flashes green. Do not open the instrument front door
when status indicator flashes green. After autosampler has stopped moving, status
indicator turns steady green and the ‘Install the Cartridge’ screen appears.
8. When the ‘Install the Cartridge’ screen appears (Figure 24), open the front door of the
instrument.
9. Remove the old Spectrum Compact CBC (if present) by pressing in on the locking tabs on
either side of the old Spectrum Compact CBC and pulling up to detach it from the deck.
15784TA
Figure 24. ‘Install the Cathode Buffer Cartridge’ screen.
10. Mount the Spectrum Compact CBC on the deck by aligning the two holes on the bottom of
the cartridge to the two circular posts protruding from the deck.
Note: The holes and the posts are of two sizes (large and small diameter), such that the
cartridge can only be inserted in one orientation.
11. Push the cartridge down until an audible click is heard and the cartridge is secured in
place.
steady green.

13. Select Next on the lower right of the footer of the ‘Place the Cartridge’ screen.
Note: Until Finish is selected, the ‘Installed Cathode Cartridge Information’ screen
consumables status indicator (see Section 2.3) will continue to display the status of the old
consumable.
Installing the Polymer

Change the polymer cartridge every 14 days to ensure optimal results. The polymer cartridge
must be changed after 16 (CE2304, CE2307) or 24 (CE2404, CE2407) injections (maximal
number of allowable injections per polymer cartridge). No washing or flushing of the capillary
cartridge is required between polymer type changes (i.e., switching between Polymer4 and
Polymer7).
Before beginning polymer cartridge replacement, peel off the foil seal from the top of the
cartridge and equilibrate to room temperature for at least 30 minutes.
Notes:
1. Wear gloves when handling the polymer cartridge and be sure to hold by the cartridge
skirt (Figure 6). Do not handle the cartridge by the syringe barrel as this may damage
the cartridge.
2. Check for polymer leaks during polymer cartridge replacement. Do not loosen the cap
of the polymer cartridge as the polymer may leak during a run. If you suspect a
polymer leak, contact Promega Technical Services.
3. Make sure that there are no air bubbles or crystals inside the polymer cartridge. Do not
to drop the polymer cartridge as this may introduce bubbles.
4. If you observe a precipitate, gently warm the polymer to dissolve the precipitate before
use.
5. Do not loosen the cap of the polymer cartridge. The polymer may leak out,
contaminating the system and affecting measurement accuracy.
1. Select Polymer on the ‘Consumables’ screen (Figure 11). This will open the ‘Installed
Polymer Cartridge Information’ screen (Figure 25).
15785TA
Figure 25. ‘Installed Polymer Cartridge Information’ screen.

2. Select Install in the footer to start the replacement wizard. This displays the ‘Polymer
15786TA
Figure 26. ‘Polymer Cartridge barcode scanning’ screen.
3. Using the Barcode Scanner, read the barcode label on the Spectrum Compact Polymer
Cartridge. Information about the Spectrum Compact Polymer Cartridge being installed is
displayed on the ‘Polymer Cartridge Information’ screen (Figure 27).
15787TA
Figure 27. ‘Polymer Cartridge Information’ screen.
4. Check the information displayed (e.g., confirm that the Spectrum Compact Polymer is
within its expiry date) and select Next on the lower right of the footer. Autosampler moves
to front of instrument and status indicator flashes green. Do not open front door of
instrument when status indicator flashes green. After autosampler has stopped moving,
status indicator turns steady green and the ‘Install the Cartridge’ screen appears.
5. When the ‘Install the Polymer Cartridge’ screen appears (Figure 28), open the front door of
the instrument.
6. Remove the old Spectrum Compact Polymer Cartridge (if present) by pulling the yellow
locking latch to the left (Figure 29) and pulling up on the old Spectrum Compact Polymer
Cartridge to detach it from the deck.

15788TA
Figure 28. ‘Install the Polymer Cartridge’ screen.
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Figure 29. Removing old polymer cartridge.
7. Mount the Spectrum Compact Polymer Cartridge on the deck by aligning the slot in the
polymer cartridge skirt with the tab in circular deck depression of the polymer delivery unit
(PDU) that receives the polymer cartridge (see triangle arrow on deck).
8. Push the cartridge down until the yellow locking latch on the left side of the PDU engages
the top of the polymer cartridge with an audible click.
steady green.
10. Select Next on the lower right of the footer of the ‘Install the Polymer Cartridge’ screen.
Note: Until Finish is selected, the ‘Installed Polymer Cartridge Information’ screen
consumable.

Installing the Capillary Cartridge

Change the capillary cartridge every 300 injections or when expiry date is reached to ensure
optimal results. Instructions provided here are for installation of a new capillary cartridge on
an instrument without a current capillary cartridge installed or where the current capillary
cartridge is going to be discarded. For instructions on changing a capillary cartridge where
the current one will be stored for future use, see instructions for Uninstalling and Storing the
Capillary Cartridge (Section 3.3).
Note: Be careful to not touch the detection window or the tips of the anode and cathode
electrodes during installation of the capillary cartridge, because they are fragile.
1. Select Capillary on the ‘Consumables’ screen (Figure 11). This will open the ‘Installed
Capillary Cartridge Information’ screen (Figure 30).
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Figure 30. ‘Installed Capillary Cartridge Information’ screen.
2. Select Install in the footer to start the replacement wizard. This displays the ‘Capillary
15791TA
Figure 31. ‘Capillary Cartridge barcode scanning’ screen.
3. Using the Barcode Scanner, read the barcode label on the Spectrum Compact Capillary
Cartridge. Information about the Spectrum Compact Capillary Cartridge being installed is
displayed on the ‘Capillary Cartridge Information’ screen (Figure 32).

15792TA
Figure 32. ‘Capillary Cartridge Information’ screen.
4. Check the information displayed (e.g., confirm that the Spectrum Compact Capillary
Cartridge is within its expiry date) and select Next on the lower right of the footer.
Autosampler moves to front of instrument and status indicator flashes green. Do not open
front door of instrument when status indicator flashes green. After autosampler has
stopped moving, status indicator turns steady green and the ‘Install the Cartridge’ screen
appears.
5. When the ‘Install the Capillary Cartridge’ screen appears (Figure 33), open the front door of
the instrument.
15793TA
Figure 33. ‘Install the Capillary Cartridge’ screen.
6. Open the oven door by turning the yellow knob on the lower left corner of the oven door
counterclockwise 180 degrees as depicted in the illustrations on the oven door (Figure 34).
Remove the previously used capillary cartridge by pulling on the yellow gripping knob in the
middle of the Spectrum Compact Capillary Cartridge. If the capillary cartridge currently
installed on the instrument will be stored for future use, follow instructions for Uninstalling
and Storing the Capillary Cartridge (see Section 3.3).

Illustrations
Yellow Oven
Door Knob
15794TA
Figure 34. Spectrum Compact yellow oven door knob.
7. Remove the protective covers from the detection unit, anode and cathode (Figure 35). Save
these if you intend to store the array outside of the instrument at a later date (see
Section 3.3).
Detection Unit Protective Cap
Capillary Cathode Storage Container
15795TA
Capillary Anode Storage Container
Figure 35. Spectrum Compact Capillary Cartridge protective covers.
8. While holding the Spectrum Compact Capillary Cartridge by its yellow gripping knob, insert
into the cut-out section in the oven unit first, followed by the bottom edge of the cartridge
into the positioning tab in the oven (Figure 36).
Cut-Out
Positioning Tab
15796TA
Figure 36. Cut-out section and positioning tabs in oven.

9. Push the detection unit into place in the detection window until it is locked in place
(Figure 37).
Note: Be sure to only push the frame of the detection unit. Do not touch the center of the
detection unit.
Push detection unit

to lock into position
15797TA
Figure 37. Fixing detection unit in place.
10. Close the oven door by turning the yellow knob on the lower left corner of the oven door
clockwise 180 degrees as depicted on the illustrations on the oven door (Figure 34).
steady green.
12. Select Next on the lower right of the footer of the ‘Place the Cartridge’ screen.
13. The Installation Completed screen for the Spectrum Compact Capillary Cartridge is
displayed (Figure 38). This screen states that a spatial calibration must be performed prior
to starting a run with the new Spectrum Compact Capillary Cartridge (see Section 4.1).
Note: Polymer filling of the new Spectrum Compact Capillary Cartridge is not performed at
this step, but must be performed during the spatial calibration (see Section 4.1). If a
polymer fill is not selected when performing a spatial calibration with a new Spectrum
Compact Capillary Cartridge that has not been previously filled with polymer, the spatial
calibration will fail.
15798TA
Figure 38. ‘Capillary Cartridge Installation Completed’ screen.


Note: Until Finish is selected, the ‘Installed Capillary Cartridge Information’ screen
consumble.
3.3 Uninstalling and Storing the Capillary Cartridge

It is possible to uninstall a capillary cartridge with less than 300 injections prior to its expiry
date and store the capillary cartridge for future use. Instructions provided here are for
uninstallation of a used capillary cartridge. These steps may be performed prior to installation
of a new unused capillary cartridge or reinstallation of a used and stored capillary cartridge.
Notes:
1. Storage of the Spectrum Compact Capillary Cartridge requires Capillary Preservation
Buffer (Cat.# CE2399).
2. The identity of the capillary cartridge being uninstalled is retained in the Spectrum
Compact System Software. When the capillary cartridge is reinstalled, all information
regarding number of injections and expiry date will repopulate when the cartridge’s bar
code is rescanned during the installation process. This information is stored on the
instrument and will not be retained if the cartridge is installed on a different
instrument.
3. Be careful to not touch the detection window or tips of the anode and cathode
electrodes during installation of the capillary cartridge, because they are fragile.
4. If anode and/or cathode ends of capillary cartridge dry out during storage,
performance may be affected. Always keep the anode and cathode ends of the
capillary cartridge immersed in Capillary Preservation Buffer when storing off of the
1. Select Capillary on the ‘Consumables’ screen (Figure 11). This will open the ‘Installed
Capillary Cartridge Information’ screen (Figure 30).
2. Select Uninstall in the footer to start the wizard. This displays the ‘Polymer Filling’ screen
(Figure 39).
3. Select Fill to fill the capillary cartridge with polymer. The status indicator flashes green
during polymer filling and returns to a steady green when complete, coincident with
activation of Next on the right hand side of the footer of the `Polymer Filling’ screen.
4 Select Next. A warning dialog stating `Autosampler is moving. Do Not open door’ is
displayed while the status indicator flashes green. The status indicator returns to steady
green when the `Removing the Cartridge’ screen is displayed (Figure 40).

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Figure 39. ‘Polymer Filling’ screen.
5. Open the instrument door when the ‘Removing the Cartridge’ screen is displayed
(Figure 40).
15800TA
Figure 40. ‘Removing the Cartridge’ screen.
6. Turn the yellow rotary oven door knob counter-clockwise 180 degrees to open the oven
door (Figure 34).
7. Pull out the detection unit to release it from its recess in the oven.
Note: Be careful to not touch the window of the detection unit.
8. Hold the yellow gripping knob on the front of the Spectrum Compact Capillary Cartridge
(Figure 41). Detach by lifting the bottom portion of the capillary cartridge out first, followed
by the top left part by the detection unit, as indicated by Step 3 of Figure 40.

15801TA
Figure 41. Removing the capillary cartridge.
9. Attach the detection unit cover on the detection unit as indicated in Step 4 of Figure 40.
10. Fill the capillary anode cover (Figure 35) with 400µl of Capillary Preservation Buffer. Slide
the filled capillary anode cover onto the anode as indicated in Step 5 of Figure 40.
11. Fill the capillary cathode cover (Figure 35) with 4ml of Capillary Preservation Buffer. Attach
the filled capillary cathode cover onto the cathode as indicated in Step 6 of Figure 40.
12. Store the uninstalled capillary cartridge upright at ambient temperature.
Notes:
1. Spectrum Compact Capillary Cartridges may be stored upright in its original packaging.
Do not discard the packaging if you intend to store capillary cartridges off-instrument
after partial use.
2. Evaporation of the Capillary Preservation Buffer may occur with prolonged storage. We
recommend replacing the Capillary Preservation Buffer periodically to prevent the
cathode and anode ends from drying out.
13. Close the door of the oven unit and the front door of the instrument. The status indicator
flashes amber while autosampler returns to home position, then returns to steady green.
Select Next on the ‘Removing the Cartridge’ screen (Figure 40), followed by Finish on the
subsequent ‘Uninstall Completed’ screen.
14. To install a new capillary cartridge, follow the instructions in Section 3.2 for “Installing the
Capillary Cartridge”.

3.4 Installing All Consumables at One Time

This section explains how to install all consumables at the same time.
1. Select Install All Consumables on the ‘Consumables’ screen (Figure 11).
2. Follow the on-screen instructions for the wizard, reading the barcode for each consumable
with the Barcode Scanner when prompted. After selecting Next on the ‘Capillary Cartridge
Information’ screen, a warning dialog stating ‘Autosampler is moving. Do not open door’ is
displayed along with status indicator flashing green. Status indicator returns to steady
green when the ‘Install the Cartridge’ screen is displayed (Figure 42).
3. When the ‘Install the Cartridge’ screen is displayed (Figure 42), open the front door. Then,
install all consumables on the instrument. See Section 3.2, Changing Consumables One at
a Time, for instructions on how to change each consumable.
4. After installing all consumables, close the front door of the instrument. Status indicator
flashes amber while autosampler returns to home position, then returns to steady green.
Select Next on the ‘Install the Cartridge’ screen (Figure 42).
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Figure 42. ‘Install All Cartridges’ screen.
5. Select Fill on the ‘Polymer Filling’ screen (Figure 39) to fill the capillary cartridge with
polymer. The status indicator flashes green during polymer filling and returns to a steady
green when complete, coincident with activation of Next on the right hand side of the
footer of the `Polymer Filling’ screen. Select Next when filling is complete.
Note: If polymer filling of the new Spectrum Compact Capillary Cartridge is not performed
at this step, it must be performed during the spatial calibration (see Section 4.1). If the
Spectrum Compact Capillary Cartridge is not filled prior to performing a spatial calibration,
the spatial calibration will fail.

Performing Calibrations 4
4.1 Spatial Calibration
A spatial calibration defines the position of each capillary on the camera image. You must
perform a spatial calibration after the installation of a capillary cartridge and before performing
a spectral calibration. A spatial calibration is also required any time the oven door has been
opened, the instrument has been moved or the polymer type has been changed.
Performing a Spatial Calibration

Caution! The instrument door must remain closed throughout the duration of the spatial
calibration. If the door is opened before the calibration is complete, the run will stop and the
calibration will need to be repeated.
Note: You have the option to fill the capillary cartridge with polymer before the calibration run.
If this option will be used, preheat the oven to facilitate capillary filling before beginning the
spatial calibration by selecting Oven Temperature in the Header (Figure 43). If insufficient
polymer remains to perform a fill of the capillary cartridge, an error message will be displayed,
indicating the polymer cartridge should be replaced.
Oven Temperature Icon
15803TA
Figure 43. Preheating oven.
1. Select Calibration on the maintenance portion of the Spectrum Compact CE System

Software ‘Main Menu’ screen (Figure 9) and select Spatial Calibration on the ‘Maintenance
Calibration’ screen (Figure 44).

Performing Calibrations
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Figure 44. ‘Maintenance Calibration’ screen.
2. On the ‘Spatial Calibration’ screen (Figure 45), check the Polymer Fill box if the capillary
cartridge needs to be filled with polymer prior to performing spatial calibration.
Notes:
1. If a new capillary cartridge has been installed, polymer fill is absolutely required if the
capillary cartridge was not filled with polymer as part of the capillary cartridge
installation process. The spatial calibration process will fail if there is no polymer in the
capillary cartridge.
2. No calibration date is displayed on the ‘Spatial Calibration’ screen unless you have
previously performed a spatial calibration with the installed capillary cartridge.
3. Select Run at the bottom of the ‘Spatial Calibration’ screen (Figure 45) to start the spatial
calibration run. During the calibration, an image of the spatial peaks for each capillary will
be displayed. The progress bar below the header will show the run progress and reach
100% when the spatial calibration is complete (Figure 46).
4. The spatial calibration may be aborted before the calibration is completed. To abort the
spatial calibration, select Abort. When the abort confirmation message is displayed, select
Yes to stop the spatial calibration. Select No to allow the spatial calibration to continue.
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Figure 45. ‘Spatial Calibration’ screen.

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Figure 46. Completed ‘Spatial Calibration’ screen.
5. The software will perform quality checks and calculate the following values, which are
displayed at the end of the spatial calibration run.
Parameter Description Threshold

Average Peak Height Average intensity value (in RFU) from the four >2100
capillaries
Min/Max Peak Height Relative standard deviation of intensity values (in >0.75
RFU) across the four capillaries
Capillary Spacing Difference between the maximum and minimum <2 pixels
spacing values from the four capillaries.

Reviewing a Spatial Calibration

Review the completed ‘Spatial Calibration’ screen (Figure 46).
1. Review the quality and status fields of the spatial calibration table.
Result Symbols Description

Invalid result—does not meet the quality check thresholds
An error message will be displayed if:
Failed • no peak(s) was (were) found.
• too many peaks were found.
• the result was off scale.
• too few peaks were found.
Passed Valid result—meets the quality check thresholds
2. If all conditions are marked as Passed, the spatial calibration was successful. If any
conditions are marked as failed, the spatial calibration has failed and must be rerun. There is
no option to select an active Finish as described below following a failed spatial calibration.
Note: If the detection window is not locked firmly into place in the detection unit of the
oven (Figure 37), the spatial calibration will fail.
3. After the results of the calibration have been verified, select Finish to open a confirmation
window. Selecting Yes will apply the spatial calibration, exit the ‘Spatial Calibration’ screen
and save a calibration report.
Notes:
1. The spatial calibration will not be saved and applied unless Yes is selected.
2. Selecting No will return you to the ‘Spatial Calibration’ screen.

4.2 Spectral Calibration

A spectral calibration is required for each set of dyes that will be analyzed on the Spectrum
Compact CE System (e.g., spectral calibration of the PowerPlex® 6C Matrix Standard for
analysis of the PowerPlex® Fusion 6C System). This calibration allows spectral deconvolution of
individual dyes by the data collection software. You should perform a spectral calibration after
installing a capillary cartridge and performing a spatial calibration. In addition, separate spectral
calibrations are required for Spectrum Compact Polymer4 and Polymer7. The Spectrum
Compact CE Software contains pre-installed dye sets from which a spectral calibration can be
initiated.
Polymer
Dye Set Name Types Color Chemistry
Promega 4-dye 4 and 7 4 Color (Fluorescein, JOE, TMR and CXR)
Promega 5-dye 4 and 7 5 Color (Fluorescein, JOE, TMR-ET, CXR-ET and WEN)
Promega 6-dye 4 and 7 6 Color (FL-6C, JOE-6C, TMR-6C, CXR-6C, TOM-6C and WEN)
T 5-dye 4 and 7 5 Color (6-FAM™, VIC®, NED™, PET™ and LIZ®)
T 6-dye 4 and 7 6 Color (6-FAM™, VIC®, NED™, SID, TAZ and LIZ®)
Q 5-dye 4 and 7 5 Color (6-FAM™, BTG, BTY, BTR and BTO)
Q 6-dye 4 and 7 6 Color (6-FAM™, BTG, BTY, BTR2, BTP and BTO)
Promega 4-dye 7 4 color (dROneTen, dRSixG, dTMR, dCXR)
sequencing
T 4-dye 7 4 Color (dR110, dR6G, dTMR and dROX)
sequencing
Filter1 4-dye 4 and 7 4 Color (Fluorescein, JOE, TMR and CXR)
Filter2 5-dye 4 and 7 5 Color (Fluorescein, JOE, TMR-ET, CXR-ET and WEN)
Filter3 4-dye 4 and 7 4 Color (6-FAM™, HEX™, NED™ and ROX™)
Filter4 4-dye 4 and 7 4 Color (6-FAM™, VIC®, NED™ and ROX™)
Filter5 4-dye 4 and 7 4 Color (5-FAM™, JOE™, NED™ and ROX™)
Filter6 5-dye 4 and 7 5 Color (6-FAM™, VIC®, NED™, PET™ and LIZ®)

Performing a Spectral Calibration

Before a spectral calibration run is started, ensure all consumables are installed and in
sufficient supply (see Section 2.3). For best quality results, use unexpired reagents that are
within the recommended use range (see Section 1.5). Select Oven Temperature in the Header
ribbon (Figure 43) to preheat the oven to 60°C.
1. Follow the instructions in the appropriate Spectrum Compact Spectral Calibration Manual
to prepare the spectral calibration samples for Promega chemistries.
Note: For spectral calibration of kits from other vendors, follow the manufacturer’s
instructions.
2. Select Calibration on the maintenance portion of the Spectrum Compact CE System
Software ‘Main Menu’ screen (Figure 9) and select Spectral Calibration on the
‘Maintenance Calibration’ screen (Figure 44).
3. Select the appropriate dye set from the ‘Dye Set List’ screen, and then select Calibration
(Figure 47).
Notes:
: Scrolls up and down by one page.
: Scrolls to first or last page.
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Figure 47. ‘Dye Set List’ screen.
Notes:
1. No calibration date is displayed in the Calibrated Dye/Dye Set column unless you have
previously performed a spectral calibration for that dye set. To view the current calibration
for a given dye set (one which has a calibration date associated with it), select the dye set
in the table and then Review. See Reviewing a Spectral Calibration below for details on the
information supplied on the review screen.
2. It is only possible to calibrate a dye set that is associated with the polymer type currently
installed on the instrument. For example, if Spectrum Compact Polymer4 is installed, the
software only allows you to calibrate a dye set that is associated with Polymer4.

15808TA
Figure 48. ‘Assemble the Cartridge’ screen.
4. Add spectral calibration samples to wells 1–4 of an 8-well strip tube, place a Strip Septa
Mat, 8-Well, on the strip tube, and place into lane position A of the strip base, ensuring that
spectral calibration sample containing wells are in position A1 to A4 as shown on the
‘Assemble the Cartridge’ screen (Figure 48).
5. Place the retainer over the strip(s) in the holder, aligning the lane names A to D and well
numbers 1 to 8 on the retainer to those on the strip base and pressing until the retainer
clicks into the strip base.
6. Select Next. A message window will open indicating that the autosampler is moving and
telling the user to not open the door. In addition, the status indicator flashes green while
the autosampler is moving. After autosampler movement is complete, the message
window closes and the status indicator returns to a steady green.
Note: Do not open the door while the autosampler is in motion.
7. Open the instrument door, and place the sample cartridge on the autosampler following
the instructions displayed on the ‘Install the Cartridge’ screen (Figure 49). Press down on
the yellow tab on the autosampler deck that locks the sample cartridge in place before
placing the sample cartridge into position. Release the tab to lock the sample cartridge in
place on the autosampler deck.
Note: If you already placed the sample cartridge in the instrument, you can move to the
‘Spectral Calibration’ Screen by selecting Next.

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Figure 49. ‘Install the Cartridge’ screen.
8. When the sample cartridge is locked into place on the autosampler, close the instrument
door and wait for the status indicator to stop flashing amber and turn steady green.
Note: Do not open the door while the autosampler is in motion. Follow the instructions
displayed on the screen.
9. After the autosampler has returned to its home position, the ‘Spectral Calibration’ screen
will automatically be displayed (Figure 50). Select Run to start the spectral calibration.
Spectral calibration runs take about 30 minutes, regardless of dye set or polymer type.
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Figure 50. ‘Spectral Calibration’ screen.
10. During the calibration, an image of the spectral peaks in each capillary will be displayed on
the ‘Raw Data’ tab. The progress bar below the header will show the run time remaining in
minutes until the spectral calibration is complete.
Note: The spectral calibration may be aborted before the calibration is completed. To abort
the spectral calibration:
a. Select Abort.
b. When the abort confirmation message is displayed, select Yes to stop the calibration.
Select No to allow the calibration to continue.

Reviewing a Spectral Calibration

The completed spectral calibration can be reviewed from the ‘Spectral Calibration’ screen
(Figure 50). There are four review tabs to choose from: Raw Data, Calibrated Data, Matrix Data
and Quality.
Note: Do not select Finish until you have evaluated the quality of the spectral calibration data.
‘Quality’ Tab
1. Select the ‘Quality’ tab to review the quality value, condition number and status for each
capillary (Figure 51).
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Figure 51. Spectral calibration ‘Quality’ tab screen.
Result Symbols Description

Invalid result
An error message will be displayed if:
• Missing peak for at least one of the expected dye-labeled
fragments.
Failed • More dye-labeled peaks than expected for the matrix
standard being run.
• The order in which dye-labeled fragments are detected is
not that expected for the dye set used.
• Signal from dye-labeled fragments is off-scale.
Passed Valid result

2. Each capillary must meet the passing criteria for Quality Value and Condition Number. The
default passing criteria set in the software are as follows.
Sequencing Spectral Calibrations

Dye Set Quality Value Condition Number
T 4-dye sequencing ≥0.95 ≤5.5
Promega 4-dye sequencing ≥0.95 ≤5.5
Fragment Analysis Spectral Calibrations

Dye Set Quality Value Minimum Condition Number Maximum
Promega 4-dye ≥0.95 ≤8.5
T 5-dye ≥0.95 ≤13.5
T 6-dye ≥0.95 ≤8.0
Q 5-dye ≥0.95 ≤20.0
Q 6-dye ≥0.95 ≤13.5
Filter1 4-dye ≥0.95 ≤8.5
Filter2 5-dye ≥0.95 ≤13.5
Filter3 4-dye ≥0.95 ≤8.5
Filter4 4-dye ≥0.95 ≤8.5
Filter5 4-dye ≥0.95 ≤8.5
Filter6 5-dye ≥0.95 ≤13.5
Spectral Calibration Criteria Definitions.
Quality Value This parameter describes the confidence with which fluorescent
signal from any given dye can be separated from that
contributed by the other fluorescent dyes present. The highest
theoretical value is 1.0, with no signal from any given fluorescent
dye contributing to signal from any of the other fluorescent dyes.
Condition Number This parameter is a measure of the degree to which there is
overlap in the spectral emission profiles of the dyes used in a
given dye set. A theoretical ideal situation would be no overlap in
emission profiles between dyes. This would result in a Condition
Number of 1.0. As the extent of overlap increases, so does
the condition number. Condition number is a function of the
dyes used in a dye set, such that each dye set has a maximum
acceptable condition number based on the dyes present in that
dye set and the extent to which their spectral emission profiles
are expected to overlap each other.

3. If all capillaries are marked as “Passed”, the spectral calibration was successful. Proceed to
the raw data review. If the data of a single capillary has failed to meet the criteria, the
quality value and condition number from a specified neighboring capillary can be borrowed
and applied to the failed capillary. If more than one capillary has failed to meet the criteria,
the spectral calibration for the capillary cartridge will fail and must be repeated.
Note: Review the data quality for each capillary in the ‘Raw Data’, ‘Calibrated Data’ and
‘Matrix Data’ tabs before allowing borrowing.
The borrowing rule is indicated in the table below.
Lender
Borrower 1 2 3 4
1 – + – –
2 – – + –
3 – + – –
4 – – + –
+ : Available
– : Unavailable
4. To borrow spectral calibration data for a failed capillary, select Borrowing in the status
column for the failed capillary.
5. The quality value and condition number from the borrowed capillary will now be displayed
in the row for the previously failed capillary, and the status of that capillary will update to
“Borrowed” with the number of the borrowed capillary indicated (Figure 52).
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Figure 52. Borrowed capillary quality data.

‘Raw Data’ Tab

1. Select the ‘Raw Data’ tab to review the raw data for each capillary (Figure 53). Select a
capillary to view from the list on the left side of the screen. Minimum peak height for a
dye-labeled fragment to be considered by the algorithm is 500 Relative Fluorescence Units
(RFU). Capillaries with peak heights less than this value will result in a failed spectral
calibration on that capillary. Also ensure that peaks are not saturating (Maximum RFU
value for raw data is 32767RFU). If peaks are saturating, dilute spectral calibration
standards before repeating the spectral calibration.
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Figure 53. Spectral calibration ‘Raw Data’ tab screen.
2. After reviewing the raw data from all capillaries, proceed to the ‘Calibrated Data’ tab.
‘Calibrated Data’ Tab

1. Select the ’Calibrated Data’ tab to review the calibrated data for each capillary (Figure 54).
Select a capillary to view from the list on the left side of the screen.
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Figure 54. Spectral calibration ‘Calibrated Data’ tab screen.
2. After reviewing the calibrated data from all capillaries, proceed to the ‘Matrix Data’ tab for
review.

‘Matrix Data’ Tab

1. Select the ‘Matrix Data’ tab to review the emission spectra for each capillary (Figure 55).
Select a capillary to view form the list on the left side of the screen.
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Figure 55. Spectral calibration ‘Matrix Data’ tab screen.
2. After the results of the calibration have been verified, selecting Finish will open a
confirmation window. Selecting Yes on the confirmation window will apply the spectral
calibration, exit the ‘Spectral Calibration’ screen, and save a calibration report.
Notes:
1. The spectral calibration will not be saved and applied unless Yes is selected.
2. Selecting No will return you to the ‘Spectral Calibration’ screen.
3. Selecting Run will rerun the spectral calibration.

Performing a Run 5
The Spectrum Compact CE System is capable of both sequencing analysis and fragment
analysis. The instructions for operating each application are very similar but will be described
separately in this manual for ease of use (for fragment analysis see Section 5.3; for sequencing
analysis see Section 5.4).
5.1 Preparing the Instrument

Before starting a run, ensure all consumables are installed and in sufficient supply for the
intended run. For best results, use unexpired reagents that are within the recommended use
range (see Section 1.5). Refer to the ‘Consumables’ screen to determine if any consumables
need to be replaced. For consumables management, see Section 3, Managing Consumables.
Ensure that a spectral calibration has been performed for the required dye set and polymer
type to be used (see Section 4.2). Select Oven Temperature in the Header (Figure 43 in Section
4.1) to preheat the oven to 60°C.
Notes:
1. We recommend you preheat the oven for at least 30 minutes prior to starting a run.
The oven will automatically turn off after 2 hours if a run is not started.
2. Do not preheat the oven if you choose to run an assay with a migration temperature
lower than 60°C. Oven can only be preheated to 60°C by selecting Oven Temperature
in the Header, so preheating oven to 60°C will overheat capillary cartridge for assay to
be run at a temperature lower than 60°C.
5.2 Preparing the Sample Cartridge

The sample setup process for the sample cartridge is the same for fragment and sequencing
analysis. Samples prepared in 8-well strip tubes are assembled into the strip base and retainer
to form the sample cartridge that is then loaded onto the instrument (see Section 2.4).

Performing a Run
5.3 Fragment Analysis

1. Select Fragment Analysis from the ‘Main Menu’ screen (Figure 56).
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Figure 56. Spectrum Compact CE System Software ‘Main Menu’ screen.
2. Enter a Run ID on the ‘Set Run ID’ screen (Figure 57). Select the Run ID box. This opens the
‘Run ID’ window, and a keypad will become active on the touch screen. Alternatively, the Run
ID can be entered using a traditional keyboard if one is connected to the Spectrum Compact
CE System. The following table lists rules for characters that can be used for a Run ID.
1 to 50 characters
Upper and lowercase alphabetic characters
Acceptable Characters
Numbers
Symbols unless listed below
Unacceptable Characters #%&{}\<>*?/$!’”:@+`|= and spaces
15817TA
Figure 57. ‘Set Run ID’ screen.

Performing a Run
3. Select Next to proceed to the message screen for placement of strips into the sample
cartridge (Figure 58).
4. Follow the message screen for placement of strips into the sample cartridge (Figure 58).
Note: Ensure that the correct strip tube is placed into the correct lane (A through D) on the
strip base and that wells 1 to 8 of the strip tube are correctly aligned with well positions 1
to 8 on the strip base (see Section 2.4).
5. Select Next to access the ‘Setup Strip Information’ screen (Figure 59).
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Figure 58. ‘Setup the Strip’ screen.
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Figure 59. ‘Setup Strip Information’ screen.
Notes:
1. There are four methods for assigning samples. The information provided here in
Section 5.3 is common for all four methods. Follow Section 5.3 first before proceeding
to one of the four methods to assign strip information in Sections 5.3.1–5.3.4.
2. The ‘Setup Strip Information’ screen is divided into two sections: Sample information
and Strip ID. You can enter sample names for samples in a strip by selecting the icon
indicating the lane (A, B, C or D) that corresponds to your samples’ strip position within
the sample cartridge. This opens the ‘Edit Strip Information’ screen (Figure 60) for the
selected lane.

Performing a Run
Assigning Sample Details to a New Strip ID

There are four methods to assign strip information. The four methods are:
• Creating new strip information
• Reusing run information from a list of completed runs
• Loading saved strip information
• Importing strip information
5.3.1 Creating New Strip Information

After selecting the desired lane (A, B, C or D) on the ‘Setup Strip Information’ screen (Figure 59),
the ‘Edit Strip Information’ screen (Figure 60) displays fields for defining the Strip ID, run assay,
sample name and sample type for that lane. Each well in the strip is represented along the left
side of the screen. The first injection set of the strip (wells 1–4) is displayed on the screen.
You can use the arrows on the right side of the screen to scroll to the second injection set
(wells 5–8). Strip information can be manually entered into this screen as described below or
loaded/imported from saved records (see Sections 5.3.3–5.3.4).
Sample Sample
Name Type
Box Icon
15820TA
Figure 60. ‘Edit Strip Information’ screen.
1. A default Strip ID is displayed. If preferred, enter a Strip ID for the selected lane by selecting
the Strip ID field. This opens the ‘Set Strip ID’ window, and a keypad will become active on
the touch screen (Figure 61). Alternatively, the Strip ID can be entered using a traditional
keyboard if one is connected to the Spectrum Compact CE System. Enter the appropriate
Strip ID, and then select OK to exit and return to the ‘Edit Strip Information’ screen. The
following table lists rules for characters that can be used for a Strip ID.
1 to 30 characters
Numbers

Performing a Run
15821TA
Figure 61. ‘Set Strip ID’ window.
2. Select a sample type on the ‘Edit Strip Information’ screen (Figure 62). Sample types must
be selected for each well position before the Sample Name box becomes active for entry
of sample name. Sample types available for fragment analysis are as follows.
Symbol Sample Type

Sample
Negative Control
Positive Control
Allelic Ladder
Unused
Note: A sample type other than “Unused” must be assigned to at least one well in each
injection set. If all of the four wells in an injection set are assigned as “Unused”, the
injection set will not be run. If all eight wells in a strip are assigned as “Unused”, a warning
message will be displayed and no strip information will be assigned. Unused wells for any
set of four wells being injected should contain formamide alone. Do not leave unused wells
empty in an injection set.
Sample Sample
Name Type
Box Icon
15822TA
Figure 62. Sample Type and Sample Name on ‘Edit Strip Information’ screen.

Performing a Run
3. To assign a sample type to a well, select the appropriate sample type button along the
bottom of the ‘Edit Strip Information’ screen (Figure 62), and then select the Sample Type
icon to the right of the sample name field for the desired well. This icon will then display the
sample type selected for that well (Figure 63).
4. Enter a sample name for each well position by selecting the Sample Name box adjacent to
the well number on the ‘Edit Strip Information’ screen (Figure 63). This opens the ‘Set
Sample Name’ window, and a keypad will become active on the touch screen (Figure 64).
Alternatively, the Sample Name can be entered using a traditional keyboard if one is
connected to the Spectrum Compact CE System. Enter the appropriate sample name, and
then select OK to exit and return to the ‘Edit Strip Information’ screen. The following table
lists rules for characters that can be used for a sample name.
1 to 50 characters
Numbers
15823TA
Figure 63. Sample Name Entry on ‘Edit Strip Information’ screen.

15824TA
Figure 64. ‘Set Sample Name’ window.

Performing a Run
5. The Spectrum Compact Control Software includes pre-loaded run assays for use with
chemistries available from Promega and other commercial suppliers. To create a new
assay or modify an existing assay, see Section 7. To assign a run assay to an injection set,
select 1st Assay on the right side of the 1st Assay field (Figure 63). This opens the ‘Select
Assay’ window (Figure 65). Select an assay from the drop-down list using the scroll
buttons to find the appropriate assay.
Notes:
: Scrolls up and down by five pages.
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Figure 65. ‘Select Assay’ window.
6. You can verify the settings of the Instrument and Analysis Protocols associated with the
assay chosen by selecting Details next to these fields (Figure 66). This will display a
window showing the settings in these protocols but will not allow you to edit these settings
(Figure 67 and Figure 68). To edit the Instrument Protocol or Analysis Protocol, see
Section 7. When the assay information is confirmed, select Apply to return to the ‘Edit Strip
Information’ screen.
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Figure 66. Accessing Instrument and Analysis Protocols on ‘Select Assay’ window.

Performing a Run
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Figure 67. ‘Instrument Protocol Details’ window.
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Figure 68. ‘Fragment Analysis Protocol Details’ window.
7. Repeat these steps for the 2nd Assay field if a second assay will be run for the strip. If not,
leave this blank.
Note: The assays available in the 2nd Assay field are filtered based on the dye set in the
assay selected in the 1st Assay field. For example, if a ‘Promega_5-dye’ dye set-based
assay is chosen in the 1st Assay field, then only assays using that same dye set are
available as an option in the 2nd Assay field. In this way, it is possible to duplicate
injections with the same assay conditions by choosing the same assay in the 2nd Assay
field as that used in the 1st Assay field. It is also possible to run duplicate injections of the
same assay conditions by using the Duplicate function of the ‘Edit Injection List’ screen
(see
Section 5.6).
8. When all information is entered and verified for the strip, select Link on the lower right
corner of the ‘Edit Strip Information’ screen (Figure 69). This will link the strip to the run. If
you want to save the Strip Information to use in future runs, save the information by
selecting Save at the bottom of the ‘Edit Strip Information’ screen (Figure 69). This will save
the strip information so that it can be loaded later into another run, as well as link the strip
to the run (see Section 5.3.3).

Performing a Run
Notes:
1. If you select Unlink without having previously selected Save at the bottom of the ‘Edit
Strip Information’ screen, you will lose the Strip Information.
2. If you forget to assign an assay in the ‘Edit Strip Information’ screen, a warning window
stating “Invalid Data Entered” will appear. Close this window, and assign an assay on
the ‘Edit Strip Information’ screen before continuing.
15829TA
Figure 69. Completed ‘Edit Strip Information’ screen.
9. Repeat Steps 1–8 for additional lanes as necessary.

10. After all the required lanes have been set up, select Next on the ‘Setup Strip Information’
screen (Figure 70).
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Figure 70. Completed ‘Setup Strip Information’ screen.
11. Proceed to Section 5.5.

Performing a Run
5.3.2 Reusing Run Information

The Spectrum Compact Control Software allows reuse of information from a completed run.
When this option is used, the strip information for all four lanes (A through D) of a previously
completed run, is copied and displayed on the ‘Setup Strip Information’ screen (Figure 70).
Note: If any strip information has already been entered into any of the four lanes (A through
D), this will overwrite that information and replace it with the information from the selected
completed run.
1. Select Load Settings at the bottom of the ‘Setup Strip Information’ screen (Figure 71) to
open the ‘Select Completed Run’ screen (Figure 72).
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Figure 71. ‘Setup Strip Information’ screen: Reusing a run.
2. Select the desired run from the list on the left side of the screen (Figure 72), and then
select Apply. This takes you back to the ‘Setup Strip Information’ screen showing the
information from the selected run.
Notes:
1. You can sort the completed run list by the Date or ID header by touching the
appropriate header.
2. Ensure that the Run ID you created in Section 5.3 is different from the one selected
from the list of completed runs in Figure 72.
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Figure 72. ‘Select Completed Run’ screen.

Performing a Run
3. The completed run information is now applied to the new run.

4. Select Next on the ‘Setup Strip Information’ screen (Figure 71).
5.3.3 Loading Saved Strip Information

The Spectrum Compact Control Software allows reuse of individual strip information saved
previously (see Step 8 of Section 5.3.1) to assign to a specific lane (A, B, C or D) on the ‘Edit
Strip Information’ screen (Figure 73).
1. After selecting the desired lane (A, B, C or D) on the ‘Setup Strip Information’ screen
(Figure 59), select Load at the bottom of the ‘Edit Strip Information’ screen (Figure 73) to
open the ‘Load Strip Information’ screen (Figure 74).
Load
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Figure 73. ‘Edit Strip Information’ screen: Loading a previously saved Strip ID.
2. Select the desired strip information from the list on the left side of the window, and then
select Apply. This will return you to the ‘Edit Strip Information’ screen. The previously saved
strip information is now applied to the new strip.
Notes:
1. You can sort the Load Strip Information list by ID or Date by touching the appropriate
header.
2. The same information from a saved Strip ID may be used multiple times within a run.
Different Strip IDs may be assigned to multiple uses of the same Strip ID in a run by
editing the Strip ID in the ‘Edit Strip Information’ screen.
3. It is also possible to use the ‘Load Strip Information’ screen (Figure 74) to delete strips
that are no longer required. Select the strip to be deleted from the list on the left side of
the window, and then select Delete. A warning window asking “Are you sure you want to
delete the strip?” will appear. Selecting Yes deletes the strip and takes you back to the
‘Load Strip Information’ screen. Selecting No closes the window and takes you back to
the ‘Load Strip Information’ screen without deleting the strip.

Performing a Run
Details of
the strip
information
selected in
the list
15832TA
Figure 74. ‘Load Strip Information’ screen.
3. When all information is entered and verified for the strip, select Link.
5.3.4 Importing Saved Strip Information

The Spectrum Compact Control Software allows you to import strip information created as an
.xml file on a personal computer using the ‘Strip Setup Tool’ (see Section 13). In this method,
strip information is assigned separately to each lane.
1. Insert a USB drive into the USB connection port in the front of the instrument.
2. Select Import at the bottom of the ‘Set Strip Information’ screen (Figure 75) to open the
‘Import Strip Information’ screen (Figure 76).
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Figure 75. ‘Setup Strip Information’ screen: Importing a strip.

Performing a Run
3. Select the desired ‘Strip File’ information from the list (Figure 76).
Notes:
1. You can sort the Import Strip Information list by Strip ID or Date by selecting the
appropriate header.
2. Import does not become active until a Strip File has been selected from the list.
3. Only strips that match the currently installed polymer type will be displayed.
15834TA
Figure 76. ‘Import Strip Information’ screen.
4. Once a Strip File has been selected, the Details for that strip are displayed on the right side
of the screen (Figure 77).
5. Select the lane icon for each lane (A, B, C or D) to display the details of that lane/strip.
6. Select Import to import the selected Strip File information. This takes you back to the
‘Setup Strip Information’ screen showing the imported strip information. 15835TA
Figure 77. ‘Import Strip Information’ screen: Strip details.


Performing a Run
5.4 Sequencing Analysis

Before beginning sequencing analysis, ensure that Spectrum Compact Polymer7 is currently
installed by selecting Consumables in the header. Sequencing analysis can only be performed
with Spectrum Compact Polymer7. If not installed, follow instructions in Section 3.2 to install a
new Spectrum Compact Polymer7 Cartridge.
1. Select Sequencing Analysis from the ‘Main Menu’ screen (Figure 78).
15816TA
Figure 78. Spectrum Compact CE System Control Software ‘Main Menu’ screen.
2. A default Run ID appears. If preferred, enter a new Run ID on the ‘Set Run ID’ screen
(Figure 79). Select the ‘Run ID’ window. This opens the ‘Set Run ID’ screen, and a keypad
will become active on the touch screen. Alternatively, the Run ID can be entered using a
traditional keyboard if one is connected to the Spectrum Compact CE System. The
following table lists rules for characters that can be used for a Run ID.
1 to 50 characters
Upper- and lowercase alphabetic characters
Numbers
15836TA
Figure 79. ‘Set Run ID’ screen.

Performing a Run
3. Select Next to proceed to the message screen for placement of strips into the sample
cartridge (Figure 80).
4. Follow the message screen for placement of strips into the sample cartridge (Figure 80),
and then select Next to access the ‘Setup Strip Information’ screen (Figure 81).
Note: Ensure that the correct strip tube is placed into the correct lane (A through D) on the
strip base and that wells 1 to 8 of the strip tube are correctly aligned with well positions 1
to 8 on the strip base (see Section 2.4).
15818TA
Figure 80. ‘Setup the Strip’ screen.
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Figure 81. ‘Setup Strip Information’ screen.
Notes:
1. There are four methods for assigning samples. The information provided here in
Section 5.4 is common for all four methods. Follow Section 5.4 first before proceeding
to one of the four methods to assign strip information in Sections 5.4.1–5.4.2.
2. The ‘Setup Strip Information’ screen is divided into two sections: Sample Information and
Strip ID. You can enter sample names for samples in a strip by selecting the icon
indicating the lane (A, B, C or D), which corresponds to your samples’ strip position within
the sample cartridge. This opens the ‘Edit Strip Information’ screen (Figure 82) for the
selected lane.

Performing a Run
Assigning Sample Details to a New Strip ID

There are four methods to assign strip information. The four methods are:
• Creating new strip information

After selecting the desired lane (A, B, C or D) on the ‘Setup Strip Information’ screen (Figure 81),
the ‘Edit Strip Information’ screen (Figure 82) displays fields for defining the Strip ID, run assay,
sample name and sample type for that lane. Each well in the strip is represented along the left
side of the screen. The first injection set of the strip (wells 1–4) is displayed on the screen. You
can use the arrows on the right side of the screen to scroll to the second injection set (wells
5–8). Strip Information can be manually entered into this screen as described below or loaded/
imported from saved records (see Sections 5.3.2–5.3.4).
Sample Sample
Name Type
Box Icon
15838TA
Figure 82. ‘Edit Strip Information’ screen.
1. A default Strip ID is displayed. If preferred, enter a new Strip ID for the selected lane by
selecting the Strip ID box. This opens the ‘Set Strip ID’ window, and a keypad will become
active on the touch screen (Figure 83). Alternatively, the Run ID can be entered using a
traditional keyboard if one is connected to the Spectrum Compact CE System. Enter the
appropriate Strip ID, and then select OK to exit and return to the ‘Edit Strip Information’
screen. The following table lists rules for characters that can be used for a Strip ID.
1 to 30 characters
Numbers

Performing a Run
15821TA
Figure 83. ‘Set Strip ID’ window.
2. Select a sample type on the ‘Edit Strip Information’ screen (Figure 84). Sample types must
be selected for each well position before the Sample Name box becomes active for entry
of sample name. Sample types available for sequencing analysis are listed in the following
table.
Sample Type Icon Sample Type

Sample
Negative Control
Positive Control
Unused
Note: A sample type other than “Unused” must be assigned to at least one well in each
injection set. If all of the four wells in an injection set are assigned as “Unused”, the
injection set will not be run. If all eight wells in a strip are assigned as “Unused”, a warning
message will be displayed and no strip information will be assigned. Unused wells for any
set of four wells being injected should contain formamide alone. Do not leave unused wells
empty in an injection set.
Sample Sample
Name Type
Box Icon
15839TA
Figure 84. Sample Type and Sample Name on ‘Edit Strip Information’ screen.

Performing a Run
3. To assign a sample type to a well, select the appropriate sample type along the bottom of
the ‘Edit Strip Information’ screen (Figure 84), and then select the Sample Type icon to the
right of the sample name field for the desired well. This icon will then display the sample
type selected for that well (Figure 85).
4. Enter a sample name for each well position by selecting the Sample Name box adjacent to
the well number on the ‘Edit Strip Information’ screen (Figure 85). This opens the ‘Set
Sample Name’ window, and a keypad will become active on the touch screen (Figure 86).
Alternatively, the Sample Name can be entered using a traditional keyboard if one is
connected to the Spectrum Compact CE System. Enter the appropriate sample name, and
then select OK to exit and return to the ‘Edit Strip Information’ screen. The following table
lists rules for characters that can be used for a sample name.
1 to 50 characters
Numbers
15840TA
Figure 85. Sample Name Entry on ‘Edit Strip Information’ screen.

15824TA
Figure 86. ‘Set Sample Name’ window.

Performing a Run
5. The Spectrum Compact Control Software includes preloaded run assays for use with
chemistries available from commercial suppliers. To create a new assay or modify an
existing assay, see Section 7. To assign a run assay to an injection set, select 1st Assay
on the right side of the 1st Assay field (Figure 85). This opens the ‘Select Assay’ screen
(Figure 87). Select an assay from the drop-down list using the scroll buttons to find the
appropriate assay.
Notes:
: Scrolls up and down by five pages.
15841TA
Figure 87. ‘Select Assay’ screen.
Note: Only select sequencing assays containing “XSeq” when using a bead-based
purification method in which the beads remain at the bottom of the wells. These assays
adjust the height of the deck during injection to keep the cathode end of the capillary
cartridge above the level of the purification beads.

Performing a Run
6. You can verify the settings of the Instrument and Analysis Protocols associated with the
assay chosen by selecting Details next to these fields (Figure 88). This will display a window
showing the settings in these protocols but will not allow you to edit these settings (Figure 89
and Figure 90). To edit the Instrument Protocol or Analysis Protocol, see Section 7. When the
assay information is confirmed, select Apply to return to the ‘Edit Strip Information’ screen.
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Figure 88. Accessing Instrument and Analysis Protocols on ‘Select Assay’ screen.
15843TA
Figure 89. ‘Instrument Protocol Details’ window.

15844TA
Figure 90. Sequencing ‘Analysis Protocol Details’ window.

Performing a Run
7. Repeat these steps for the 2nd Assay field if a second assay will be run for the strip. If not,
you can leave this blank.
Note: The assays available in the 2nd Assay field are filtered based on the dye set in the
assay selected in the 1st Assay field. For example, if a ‘T 4-dye sequencing’ dye set-based
assay is chosen in the 1st Assay field, then only assays using that same dye set are
available as an option in the 2nd Assay field. In this way, you can duplicate injections with
the same assay conditions by choosing the same assay in the 2nd Assay field as that used
in the 1st Assay field. you can also run duplicate injections of the same assay conditions
by using the Duplicate function of the ‘Edit Injection List’ screen (see Section 5.6).
8. When all information is entered and verified for the strip, select Link on the lower right corner
of the ‘Edit Strip Information’ screen (Figure 91). This will link the strip to the run. If you want
to save the Strip Information to use in future runs, you will need to save the information by
selecting Save at the bottom of the ‘Edit Strip Information’ screen (Figure 91). This will link
the strip to the run but will also save that Strip ID so that it can be loaded later into another
run (see Section 5.3.3).
Notes:
1. If you select Unlink without having previously selected Save at the bottom of the ‘Edit
Strip Information’ screen, you will lose the Strip Information.
2. If you forget to assign an assay in the ‘Edit Strip Information’ screen, a warning window
stating “Invalid Data Entered” will appear. Close this window, and assign an assay on
the ‘Edit Strip Information’ screen before continuing.
15845TA
Figure 91. Completed ‘Edit Strip Information’ screen.

10. After all the required lanes have been set up, select Next on the ‘Setup Strip Information’
screen (Figure 92).

Performing a Run
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Figure 92. Completed ‘Setup Strip Information’ screen.
5.4.2 Reusing/Loading/Importing Previous Run Information

There are three additional methods to assign strip information for a sequencing run.

These methods are the same as those described in Section 5.3 for fragment analysis. For
information on how to use these methods, see Section 5.3.2, 5.3.3 or 5.3.4, as appropriate.
5.5 Loading the Sample Cartridge

1. After selecting Next on the ‘Setup Strip Information’ screen, a message window will open
indicating that the autosampler is moving and telling you to not open the door. In addition,
the status indicator flashes green while the autosampler is moving. After autosampler
movement is complete, the message window closes and the status indicator returns to a
steady green.
Note: Do not open the door while the autosampler is in motion.

Performing a Run
2. Open the instrument door, and then place the sample cartridge on the autosampler
following the instructions displayed on the ‘Install the Cartridge’ screen (Figure 93). Press
down on the yellow tab on the autosampler deck that locks the sample cartridge in place
before placing sample cartridge into position. Release the tab to lock the sample cartridge
in place on the autosampler deck.
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Figure 93. ‘Install the Cartridge’ screen.
3. When the sample cartridge is locked into place on the autosampler, close the instrument
door and wait for the status indicator to stop flashing amber and turn steady green.
Note: Do not open the door while the autosampler is in motion. Follow the instructions
displayed on the screen.
4. After the autosampler has returned to its home position, the ‘Edit Injection List’ screen will
be displayed (Figure 94). To edit the injection list, see Section 5.6.
5. Select Run to start the run. A confirmation message is displayed. Select Yes to start the
run. Select No to return to the ‘Edit Injection List’ screen.
15848TA
Figure 94. ‘Edit Injection List’ screen.

Performing a Run
5.6 Editing Injection Information Prior to Starting a Run

The ‘Edit Injection List’ screen (Figure 94) allows users to change the run assay assigned to
the linked strips prior to starting the run. You can also remove, duplicate or reorder injections
from this screen. By default the injection list displays all scheduled injections in order by lane
and well position. You can use the arrows on the right side of the screen to locate a specific
injection.
5.6.1 Changing the Assigned Run Assay

1. Select the appropriate injection in the list (Figure 94), and then select Edit to open the
‘Select Assay’ window.
2. Select a different assay as needed. See Step 5 of Section 5.3.1, Fragment Analysis, or
Section 5.4.1, Sequencing Analysis.
3. Select Apply in the ‘Select Assay’ window to assign the assay to the injection.
5.6.2 Removing an Injection from the Injection List

1. Select the appropriate injection in the list (Figure 94), and then select Remove.
2. Select Yes or No on the Confirmation Screen.
Note: Remove does not become active when selecting an injection if there is only one
injection in the run.
5.6.3 Duplicating an Injection in the Injection List

Select the appropriate injection in the list (Figure 94), and then select Duplicate. The duplicate
injection is added to the bottom of the injection list.
Note: Duplicating injections from this screen adds scheduled injections to the bottom of
the list. If the maximum use count of a polymer will be exceeded by adding these
injections, the run will not be allowed to start.
5.6.4 Reordering Injections in the Injection List

1. Select the appropriate injection in the list, and then touch or at the bottom left of
the ‘Edit Injection List’ screen (Figure 94) to change the order.
2. When all injection edits are complete, select Run to start the run.

Performing a Run
5.7 Monitoring a Run

The ‘Monitor Run’ screens (Figure 95) are automatically displayed after a run is started. You
can monitor the status of a run from one of the four tabs on the screen: Progress, Injection
List, Monitor and Result. Information displayed on these screens is the same for fragment and
sequencing analysis, except for the ‘Results’ screen.
15849TA
Figure 95. ‘Monitor Run’ screens.
Note: Skip Injection and Stop Injection do not become active in footer until the first
injection of the run has started.

Performing a Run
On the ‘Monitor Run’ screens, the injection progress, data evaluation, sample types and
injection status are indicated by various symbols as shown in the following table.
Symbol Description
Waiting for Injection
Injection in Progress
Injection in Progress (Nth
time)
Injection progress Injection Completed

(completed without an error)
Injection Failed (an error
has occurred) or Injection
Aborted
Injection Skipped
Note: Green check mark
only applied to samples with
offscale data. For samples
with data that is not offscale,
Data evaluation this column is left blank.
Failed Data Analysis (some
evaluation item failed)
Questionable Data (some
evaluation item did not pass)
Sample
Negative Control
Sample type Positive Control
Allelic Ladder (Fragment only)
Unused
Injection in Progress
Injection status
Duplicated Injection

Performing a Run
‘Progress’ Tab
The ‘Progress’ tab displays the same information as the ‘Setup Strip Information’ screen of the
setup process (see Sections 5.3 and 5.4) with some additional status information. The injection
status for each assigned injection will update as the run progresses as displayed in this tab.
Selecting an injection set will display strip information details on the right side of the screen.
Here, you can review the assigned strip information as well as the remaining injection time.
This tab also provides options in the footer for skipping or stopping an injection or aborting
the run using the buttons at the bottom of the screen (Figure 96). Skipping an injection will
immediately end the injection in progress and proceed to the next scheduled injection.
Stopping an injection will complete the injection in progress and then pause the run. Skip
Injection, Stop Injection and Abort are greyed out after selecting Stop Injection. After
completion of stopped injection, Stop Injection transitions to become Resume (Figure 97). The
run will resume after you select Resume. Selecting Abort will immediately end the injection in
progress and cancel all remaining scheduled injections of the run.
Note: When a run is aborted, the data from any completed injections of the aborted run
remains saved.
15850TA
Figure 96. ‘Progress Tab’ footer.
15851TA
Figure 97. ‘Progress Tab’ footer with Resume active.

Performing a Run
‘Injection List’ Tab
The ‘Injection List’ tab (Figure 98) displays the same information as the ‘Edit Injection List’
screen (Figure 94) of the setup process (see Section 5.5) with additional status information
and the same footer buttons as on the ‘Progress’ tab. From the ‘Injection List’ tab it is possible
to edit runs in the same manner as the setup process (see Section 5.6). The options to
duplicate, reorder, remove or edit injection information depends on the status of an injection.
Status Injection Completed Injection in Progress Waiting for Injection

Duplication o o o
Reorder x x o
Removal x x o
Editing x x o
o: Available
x: Unavailable
15852TA
Figure 98. ‘Injection List’ tab.
Notes:
1. Duplicate only becomes active when one of the injections in the list is selected.
Remove, Edit and Order only become active when injections in the list that have not
been completed or are not in the process of being run are selected.
2. If the injection that you are currently editing is about to be processed, the run is
paused. Selecting Resume after editing it will restart the run.

Performing a Run
‘Monitor’ Tab
The ‘Monitor’ tab displays the real-time raw data electropherogram for the samples currently
being run (Figure 99). Data are plotted in RFUs vs scan number (data points). The injection
number, lane and well assignment, and sample name are displayed at the top of the
electropherogram. You can use Previous Sample and Next Sample at the bottom of the screen
to navigate through the samples of an injection.
Note: Only data from the current injection is displayed. To view data from previous completed
injections from the run, touch the ‘Results’ tab.
15853TA
Figure 99. ‘Monitor’ tab.
The colors of the peak wavelengths differ between sequencing analysis and fragment analysis.
• Sequencing (4 colors): A/green, C/blue, G/black, T/red

• Fragment (4/5/6 colors): blue, green, yellow, red, orange (5- and 6-color), purple (6-color)
Note: For easy visualization of sequencing analysis data, the yellow dye channel is displayed as
black on the screen. For fragment analysis, the yellow dye channel is represented as yellow.
‘Result’ Tab
Results of completed injections can be viewed from the ‘Result’ tab of a current run and can
be viewed at any time during the run. The following information is displayed for fragment and
sequencing analysis.

Performing a Run
Analysis Type Item Description

Fragment File Name Name of saved data file
Result Overall evaluation (Pass/Suspect/Fail)
Displays the results of the initial analysis of the sizing
quality (SQ) and electrophoresis quality (EQ).
SQ SQ is determined by comparing the fragment pattern
observed for the size standard being used against that
specified for the size standard in the Sizecalling Protocol
(see Section 7.2.3). Values are from 0 to 1. Passing,
suspect and failing specifications for SQ values are set in
the Sizecalling protocol (see Section 7.2.3).
EQ EQ is the size (bases) at which the peak width at half
maximal height is equal to the distance between two
bases as calculated from the size standard.
Note: Accurate calculation of EQ by this method is
dependent on using the same size standard in the
sample that is specified in the assay used to run that
sample. Failure to use the correct size standard can
result in an erroneously failing EQ value.
Offscale Indicates whether or not sample contains offscale data
(saturation). Green check mark indicates offscale data.
For samples with data that is not offscale, this column is
left blank.
Well Lane and well position of sample
Sequencing File Name Name of the saved data file
Result Overall data evaluation (Pass/Suspect/Fail)
Displays the lowest sequencing quality flag from the
initial analysis of the Contiguous Read Length (CRL),
Trace Score and QV20+ (see Section 7.1).
CRL Number of contiguous bases in the sequence that have
an average quality value (QV) score ≥20 over a 21 base
sliding window.
QV20+ Total number of bases with a QV score from the
basecaller of at least 20 (i.e., base call accuracy of at
least 99%).
Trace Score Average QV score across bases in clear range (as defined
in basecalling protocol; see Section 7.2.2).
Well Lane and well position of sample
Use the scroll buttons on the right side of the list to review the summary results for each
sample in the run (Figure 100 and Figure 101).

Performing a Run
15854TA
Figure 100. Fragment Analysis ‘Result’ tab.
15855TA
Figure 101. Sequencing Analysis ‘Result’ tab.
Raw or analyzed data for a sample can be viewed from the ‘Result’ tab. The process is similar
for sequencing and fragment analysis data.
Application Data Type Description

Fragment Raw Displays electropherogram peaks that have been spectrally
separated, but the baselines have not been normalized.
Analyzed Primary analysis view displays electropherogram data with
baseline normalization applied after the spectral separation.
Sequencing Raw Displays the electropherogram peaks prior to any mobility
correction.
Analyzed Primary analysis view displays electropherogram data with
mobility correction and after basecalling.

Performing a Run
1. Select the appropriate sample from the review table (Figure 100 and Figure 101), and then
select View in the footer to open the ‘Graph’ screen.
2. The ‘Graph’ screen can be navigated using the icons on the screen. Some of these icons
are only available in the analyzed data view.
Icon Description
Data Toggle Button; switch between raw data and analyzed fragment data
Data Toggle Button; switch between raw data and analyzed sequencing data
Switch Mode Button; switch between the zoom mode and color palette
Quick scroll to left
Scroll to left
Scroll to right
Quick scroll to right
Switch the zoom in/zoom out direction (X and Y axis together; X only; Y only)
Zoom in button
Zoom out button
Reset View button (after zooming)
Switch on or off the peak size labeling for the internal lane standard fragments
Increase peak signal button (analyzed sequencing data only; increases signal in
Y axis without changing X axis)
Decrease peak signal button (analyzed sequencing data only; decreases signal
in Y axis without changing X axis)
Resets peak signal to original height range after touching the increase or
decrease peak signal button (analyzed sequencing data only; resets signal in Y
axis without changing X axis)
Scroll up
Scroll down
Show/Hide Blue dye channel
Show/Hide Green dye channel
Show/Hide Yellow dye channel * Displayed only for fragment analysis
Show/Hide Red dye channel
Show/Hide Purple dye channel * Displayed only for fragment analysis
Show/Hide Orange dye channel * Displayed only for fragment analysis
Show/Hide Black dye channel * Displayed only for sequencing analysis

Performing a Run
3. The raw data electropherogram is the default view of the ‘Graph’ screen. To view the
analyzed data electropherogram, select the data toggle button in the upper left corner of
the screen to toggle between raw and analyzed views (Figure 102, Figure 103, Figure 104
and Figure 105).
4. Zoom in and Zoom out work to activate either function. Both functions are turned off
initially. Selecting either button once activates that function. Selecting the same button
again (or any other button on the screen) will deactivate that function.
5. When zooming in or out, first select the appropriate direction in which you wish to zoom by
selecting the Zoom in/Zoom out direction button to toggle between the three zoom
options (zoom in X and Y axis together, X axis only or Y axis only).
Note: Selecting the Zoom in/Zoom out direction button after selecting either Zoom in or
Zoom out will deactivate the previously activated zoom in or zoom out function.
6. Select either Zoom in or Zoom out as desired to activate that function.
7. Select the screen at the point where you wish to zoom in or zoom out. The more you select
the same spot on the screen, the greater the zoom (in or out) at that point on the screen.
8. To return to the original unzoomed view, select Reset View.
15856TA
Figure 102. Fragment Analysis ‘Result’ tab raw data.

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Figure 103. Fragment Analysis ‘Result’ tab analyzed data.

Performing a Run
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Figure 104. Sequencing Analysis ‘Result’ tab raw data.
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Figure 105. Sequencing Analysis ‘Result’ tab analyzed data.
9. You can use Previous Sample and Next Sample in the footer (Figure 102, Figure 103,
Figure 104 and Figure 105) to navigate through the samples of a run. To return to the
‘Result’ tab, select Back in the footer.

Performing a Run
5.8 Exporting Results from Current Run

After reviewing data from the ‘Review’ tab, you can export the primary analysis results of the
whole run or selected samples in the run to a USB drive inserted into the storage USB port on
the front of the instrument (Figure 1).
Notes:
1. W
hen exporting selected samples, duplicate sample file names are not allowed during the
export process, and it is not possible to change the file name of the exported data. If a file
with the same name exists in the destination location for the saved data, a confirmation
message will be displayed asking if it is OK to overwrite.
2. Run results can be exported when all injections of a run are complete or when a run is
paused. If results are exported when a run is paused, only the completed injections will
be available for export. When a run is still in progress, results from individual samples
of completed injections within the ongoing run may be exported one at a time (see
Section 5.8.1).
5.8.1 Exporting One Sample at a Time

1. From the ‘Result’ tab, select the specific sample from the displayed list (Figure 100 and
Figure 101).
2. Select Export in the footer of the ‘Result’ tab screen. The sample file will be exported to the
USB drive and stored in a folder named “Run”.
3. Select USB in the header before removing the USB drive from the storage USB port.
4. When all results have been reviewed and/or exported, select Close to exit the ‘Monitor Run’
screen and return to the ‘Main Menu’ screen.
Note: This step may be omitted if the run is still in progress so that the user can continue
to monitor the rest of the injections from the run on the ‘Monitor Run’ screen.
5.8.2 Exporting Entire Run

1. At the end of the run, the ‘Progress’ tab displays Export Run in the footer (Figure 106).
Select Export Run in the footer of the ‘Progress’ tab screen. The sample files will be
exported to the USB drive and stored in a folder named “Run”.
3. When all results have been reviewed and/or exported, select Close to exit the ‘Monitor Run’
screen and return to the ‘Main Menu’ screen.
15860TA
Figure 106. ‘Progress’ tab footer with Export Run button.

Reviewing Completed Runs 6
The ‘Run List’ screen contains a list of all completed runs saved to the Spectrum Compact
Control Software. To access this screen, select Run Results on the ‘Main Menu’ screen
(Figure 9).
6.1 Reviewing Run Results

The ‘Run List’ screen is divided into two main sections: Run List and Run Details (Figure 107).
15861TA
Figure 107. ‘Run List’ screen.
Note: Delete, Export Run and View do not become active until a run is selected in the ‘Run List’
screen.
The Run List can be filtered and sorted using the buttons at the top of the list.
Header Function
Filter (All Applications, Sequencing, Toggle to filter the Run List by selected type:
Fragment) sequencing, fragment or all applications
Date Sorts the Run List by either ascending or descending
order based on the Run Date
ID Sorts the Run List by either ascending or descending
order based on the Run ID

Reviewing Completed Runs
The footer provides three options for run record management.
Command Function
Delete Deletes the selected run
Export Run Exports the selected run
View Opens the ‘Result View’ screen for the selected run record
1. Use the scroll buttons on the right side of the Run List to locate the completed run you
wish to review.
2. Select the run in the Run List corresponding to the run you wish to review. This will display
the run summary in the Run Details section of the ‘Run List’ screen.
3. Select View in the footer to view a list of samples in that run in the ‘Result View’ screen
(Figure 108). View and Export do not become active until a sample is selected.
15862TA
Figure 108. ‘Result View’ screen.
4. Use the scroll buttons on the right side of the sample list to locate the sample to review.
5. Select the sample in the File Name corresponding to the run you wish to review, and then
select View in the footer to review the electropherogram data of the sample (Figure 109).
15863TA
Figure 109. Sample-specific ‘Result View’ screen.
Note: Figure 109 has peak size labeling for the internal lane standard fragments turned on.

6. The electropherogram screen displays the raw and analyzed electropherogram data of the
selected sample. See ‘Result’ Tab in Section 5.7, Monitoring a Run, for a description of the
functions of the different screen icons/buttons.
7. Use Previous Sample and Next Sample in the footer to navigate through the samples of a
run.
8. Use Back to return to the ‘Result View’ screen (Figure 108), which displays a list of all runs
saved on the instrument.
6.2 Exporting Run Results

After reviewing data, you can export the primary analysis results of the entire run or selected
samples in the run to a USB drive inserted into the storage USB port on the front of the
instrument (Figure 1).
Note: Data may also be downloaded directly to a PC connected to the Spectrum Compact CE
System using the Spectrum Compact CE System Remote Access Software (see Spectrum
Compact CE System Remote Access Software Technical Manual #TMD064).
6.2.1 Exporting One Sample at a Time

Note: Duplicate sample file names are not allowed during the export process, and it is not
possible to change the file name of the exported data. If a file with the same name exists in the
destination location for the saved data, a confirmation message will be displayed asking if it is
OK to overwrite.
1. From the ‘Result View’ screen (Figure 108), select the specific sample from the displayed
list.
2. Select Export in the footer of the ‘Result View’ screen (Figure 108). The sample file will be
6.2.2 Exporting Entire Run

1. From the ‘Run List’ screen (Figure 107), select the desired run from the displayed list.
2. Select Export Run in the footer of the ‘Run List’ screen (Figure 107). The sample file will be
Notes:
1. For in-progress runs, if the run has been paused by selecting Stop, the results can be
exported. Only results from completed injections in the paused run can be selected. It
is not possible to export results from an injection canceled by selecting Abort.
2. Results from an in-progress injection of a current run cannot be exported.

6.3 Deleting Run Results

After reviewing and exporting data, you can delete the entire run from the instrument by
selecting the desired run name in the ‘Run List’ screen (Figure 107) and then selecting Delete. A
warning window will appear asking if you are sure you want to delete the selected data. Select
Yes to delete and No to cancel the deletion.
6.4 Reviewing Log Information

The Spectrum Compact Control Software logs alarm, consumables and operation information
for the instrument. These logs can be accessed by selecting Log, which is located in the
Review section of the ‘Main Menu’ screen (Figure 9) of the Spectrum Compact Control
Software. There are three functions available in the ‘Log’ screen (Figure 110):
1. Alarm
2. Consumables
3. Operation
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Figure 110. ‘Log’ screen.

6.4.1 Reviewing Alarm Logs

1. Select Alarm on the ‘Log’ screen (Figure 110) to open the ‘Alarm Log’ screen (Figure 111).
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Figure 111. ‘Alarm Log’ screen.
2. Select the DateTime column of the ‘Alarm Log’ screen to sort logs by date in ascending or
descending order (Figure 111).
3. Select a specific Alarm Log in the list followed by Details (becomes active after selecting
an Alarm Log) at the bottom of the screen to review the details of that specific alarm
(Figure 112).
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Figure 112. ‘Alarm Detail’ screen.

The ‘Alarm Detail’ screen provides the following information:
Information Description
Date/Time/Code Date and time the alarm occurred and the alarm code (see
Section 11 for error code list)
Level Critical Alarm—a severe condition, such as
instrument malfunction, has occurred.
Error Alarm—an error preventing electrophoresis

has occurred.
Warning—something needs attention, but the

instrument will continue operation.
Details Describes what caused the alarm.

Recommended Action Describes the recommended corrective action(s) to resolve the
issue.
4. Check the information displayed in the Details and Recommended action section of the
‘Alarm Detail’ screen (Figure 112). Perform corrective measures required to address the
information displayed. See Section 11 for a list of error codes and responses.
5. To view information for the previous or next alarm, select Previous or Next, respectively.
6. Select Close to return to the ‘Alarm Log’ screen.
7. Logs are saved to a folder called LogInfo on the USB drive.
6.4.2 Reviewing Consumables Logs

1. Select Consumables on the ‘Log’ screen (Figure 110) to open the ‘Consumables Log’
screen (Figure 113).
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Figure 113. ‘Consumables Log’ screen.
2. Select the DateTime column of the ‘Consumables Log’ screen to sort logs by date
(Figure 113).

3. Select a specific Consumables Log in the list followed by Details (becomes active after
selecting a Consumables Log) at the bottom of the screen to review the details of that
specific log (Figure 114).
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Figure 114. ‘Consumables Detail’ screen.
6.4.3 Reviewing Operation Logs

1. Select Operation on the ‘Log’ screen (Figure 110) to open the ‘Operation Log’ screen
(Figure 115).
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Figure 115. ‘Operation Log’ screen.
2. Select the DateTime column of the ‘Operation Log’ screen to sort logs by date in ascending
or descending order (Figure 115).
3. Select a specific Operation Log in the list followed by Details (becomes active after
selecting an Operation Log) at the bottom of the screen to review the details of that
specific log (Figure 116).

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Figure 116. ‘Operation Detail’ screen.
6.4.4 Exporting All Log Info

1. Select either Alarm, Consumable or Operation on the ‘Log’ screen (Figure 110).
2. Select Export (without selecting a specific Alarm, Consumable or Operation log) to export
all log information in one zipped file (i.e., not specific to a given Alarm, Consumable or
Operation log) to a USB drive. Logs are saved to a folder called LogInfo on the USB drive.
3. Select USB in the header before removing the USB drive from the USB storage port.

Managing Assays, Protocols and Dye
Sets 7
Instrument assays and protocols are managed through the Protocols menu, which is accessed
through the ‘Main Menu’ screen (Figure 9). The Protocol menu contains three submenus:
• New & Edit Protocols

• Import Protocols
• Export All Protocols
Assays or protocols can be created, edited, deleted or imported using these submenus.
Six types of assays, protocols and dye sets are used by the Spectrum Compact Control
Software:
1. Assay
2. Instrument Protocol
3. Basecalling Protocol
4. Sizecalling Protocol
5. Size Standard Protocol
6. Dye Set
The Spectrum Compact CE System comes with a series of preloaded assays, protocols and
dye sets of each type. Preloaded assays, protocols and dye sets are locked and cannot be
edited or deleted. Users have the ability to define their own assays, protocols and dye sets,
which can be edited or deleted. Both preloaded and user-created assays and protocols can
be exported to an external storage device, such as a USB drive. Only user-created assays
and protocols can be imported from an external storage device such as a USB drive into a

Managing Assays, Protocols and Dye Sets
Type Description
Assay1 An assay is comprised of application type (sequencing or fragment),
instrument protocol, polymer type, dye set and analysis protocol
required for data collection. The analysis protocol used depends on
the application as follows.
• Fragment: Sizecalling Protocol
• Sequencing: Basecalling Protocol
Instrument Protocol Defines the instrument settings to be applied during a run. This
includes: application type (sequencing or fragment), polymer type,
injection conditions and electrophoresis conditions.
Basecalling Protocol The initial analysis protocol required for sequencing applications.
Defines parameters for assigning base calls to data peaks.
Sizecalling Protocol The initial analysis protocol required for fragment applications.
Defines the parameters for assigning size calls to data peaks.
Size Standard Protocol Defines size of DNA fragments of known lengths. Used to generate a
sizing curve by which unknown fragments are sized.
Dye Set Create or edit new or existing dye sets.
1
Assays are created by associating a specific instrument protocol with a specific analysis protocol. If the instrument
and analysis protocols are added from the library, a copy of these protocols is added to the assay, such that they
can be modified within the created assay independently from the original items stored in the library. That is, changes
made to the instrument and analysis protocol within the newly created assay do not affect the instrument and
analysis protocols stored in the library.
7.1 General Settings and Protocol Security Symbols

Depending on the security setting (see Section 8), symbols on the protocol screens change
automatically as shown in Section 7.1.1.
7.1.1 Protocol Security Symbols

Protocol Type Security Setting
High Normal
Pre-loaded
User-defined Owner1 No symbol displayed
Other than the owner No symbol displayed No symbol displayed

Lock status2 Locked No symbol displayed
Unlocked No symbol displayed No symbol displayed
1
User-defined protocols created by the individual logged into the system.
2
Assays and protocols created under high-security settings by a user without administrative rights are locked from
other users without administrative rights but not from users with administrative rights.

7.1.2 Filtering and Sorting in the List

The list of assays or protocols displayed in the assay and protocol lists can be filtered based on
application type (all applications, fragment or sequencing) and library type (all libraries,
pre-loaded or user-defined). By repeatedly selecting the appropriate button it is possible to
toggle between filter options.
Default Filter Lists Displaying

Button Setting Filter Setting Order Filter Button
All Applications 1. All Applications Assay
2. Sequencing Instrument Protocol
3. Fragment
All Libraries 1. All Libraries Assay
Instrument Protocol
2. Pre-loaded
Basecalling Protocol
3. User-Defined Sizecalling Protocol
Size Standard Protocol
Dye Set
Protocols may also be sorted alphanumerically (toggle between ascending and descending
order by selecting the sort button) based on Date, ID, Run Module name or Size Standard
name.
Assays and Protocols

Sort Button Sorting with Sorting Function
Date By Date (Month/Day/Year) Assay
Instrument Protocol
Sizecalling Protocol
ID By ID Assay
Instrument Protocol
Sizecalling Protocol
Run Module By Run Module Name Instrument Protocol
Size Standard By Size Standard Name Sizecalling Protocol

7.1.3 Rules for Characters Used to Name Assays, Protocols and Dye Sets
The following table lists rules for characters that can be used when naming new assays and
protocols.
1 to 40 characters
Numbers
7.2 Creating Protocols, Assays and Dye Sets

Select New & Edit Protocols on the ‘Main Menu’ screen (Figure 9) to access the ‘New & Edit
Protocols’ screen (Figure 117). Instrument, Basecalling, Sizecalling and Size Standard protocols
and Dye Sets should be defined for appropriate applications prior to creating a new assay.
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Figure 117. ‘New & Edit Protocols’ screen.

7.2.1 Creating a New Instrument Protocol

1. Select Instrument Protocols in the ‘New & Edit Protocols’ screen (Figure 117). This will
open the ‘Instrument Protocol List’ screen (Figure 118).
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Figure 118. ‘Instrument Protocol List’ screen.
2. Select Create in the footer to open the ‘New Instrument Protocol’ screen (Figure 119).
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Figure 119. ‘New Instrument Protocol’ screen.

3. The ‘New Instrument Protocol’ screen displays the detailed parameters of the protocol.
Minimum Maximum
Parameter Information Value Allowed Value Allowed
Protocol ID Defines the protocol name 1 Character 40 Characters
Application Type Defines whether the protocol is for NA NA
Sequencing or Fragment analysis.
Polymer Type Allows selection of Polymer4 or Assigned using Assigned using
Polymer7 through drop-down box. the drop-down the drop-down
menu menu
Run Module Pre-loaded modules that specify Assigned using Assigned using
run condition parameters the drop-down the drop-down
(injection voltage, run voltage, menu menu
oven temperature, injection time,
run time and delay time). Each of
these parameters can be edited
from run module default value.
Injection Voltage (kV) Defines the injection voltage 1 15
Run Voltage (kV) Defines the voltage applied during 1 18
electrophoresis
Oven Temperature (°C)1 Defines the target oven 40 70
temperature setting for the
protocol
Injection Time (sec) Defines the injection duration 1 600
Run Time (sec) Defines the time needed to 300 7200
complete the run and collect data
from all labeled fragments
Delay Time (sec) Defines the time to delay data 1 3600
collection while fragments travel
from the capillary tips to the
detection window
1
Changing the oven temperature in the protocol does not change the preheating temperature.
4. Enter a Protocol ID, and then select or enter the appropriate settings for the new
instrument protocol.
5. Select Save to close the ‘New Instrument Protocol’ screen and return to the ‘Instrument
Protocol List’ screen.

7.2.2 Creating a New Basecalling Protocol

1. Select Basecalling Protocols in the ‘New & Edit Protocols’ screen (Figure 117). This opens
the ‘Basecalling Protocol List’ screen (Figure 120).
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Figure 120. ‘Basecalling Protocol List’ screen.
2. Select Create in the footer to open the ‘New Basecalling Protocol’ screen (Figure 121).
There are four tabs on the ‘New Basecalling Protocol’ screen.
Tab Description
Mixed Bases Setting Checking the “Use Mixed Base Identification” box enables this
function (Figure 121). If there are two peaks at the same position
and the smaller intensity peak is greater than the Secondary
Peak Height Threshold (height as a percentage of the major peak
at the same position) set in the basecalling protocol, then the
software will identify this peak as a mixed base.
Minimum and maximum values allowed for the Secondary Peak
Height Threshold are 1% and 99%, respectively.

Tab Description
Clear Range Checking the “Use Clear Range” box enables the user to define
First bp–Last bp the first and last bp using the fields in the clear range diagram
(Figure 123 and Figure 124).
Note: When creating a new Basecalling Protocol, the default
setting for Clear Range First bp-Last bp is disabled (box
unchecked).
When using the ‘Clear Range First bp–Last bp’ method in the
basecalling protocol, the first bp position to be considered for
analysis is set by entering the 5´ bp position in the ‘First bp’ field.
For the 3´ end point (last bp position to be considered for
analysis), two last bp setting methods are available for setting
the 3´ end of the clear range:
• Last bp: Enter the final base in the sequence to be considered
for analysis (enter 3´ bp position in ‘Last bp’ field) (Figure 123).
• Bases to trim from 3´ end: Trims the specified number of bases
from the 3´ end of the sequence run to determine the last bp
to consider for analysis (enter number of bases to trim in ‘bp’
field) (Figure 124).
Minimum and maximum values allowed by software for ‘First
bp’, ‘Last bp’ and ‘Bases to trim from 3´ end’ fields are 1bp and
1200bp, respectively.
Clear Range Checking the “Use Quality Values” box defines the first and last
Quality Value bp using the quality value specified (Figure 125).
Note: When creating a new Basecalling Protocol, the default
setting for Clear Range Quality Value is disabled (box
unchecked).
The software creates a clear range by removing bases from the
5´ and 3´ end of the read based on QV values. In the resulting
clear range, no sliding window of ‘bases out of’ (e.g., 30) will
contain more than the specified number of bases (e.g., 4 in the
‘fewer than’ field) with a QV value below that set in the ‘have QVs
less than’ field (e.g., 20) (Figure 125). Any sliding 30 base window
in the first or last part of the sequence that does not meet these
parameters is trimmed from these ends.
Minimum and maximum values allowed by software for ‘fewer
than’ and ‘bases out of’ fields are 1bp and 1,200bp, respectively.
The value entered in the ‘fewer than’ field must always be less
than the ‘bases out of’ field.
Minimum and maximum values allowed by software in the ‘have
QVs less than’ field are 1 and 60, respectively.

Tab Description
Sequencing Quality Defines the CRL, QV20+ and Trace Score values for passing and
failing data (Figure 126). Data that fall between these values will
be flagged as “Suspect” (data should be manually reviewed in
‘Result’ tab to determine whether or not it is acceptable to the
user or requires reinjection). See ‘Result’ Tab in Section 5.7 for
definition of CRL, QV20+ and Trace Score.
Minimum and maximum values allowed by software for CRL are
1bp and 800bp, respectively. The value entered in the ‘Fail’ field
must always be less than the ‘Pass’ field.
Minimum and maximum values allowed by software for QV20+
are 1bp and 800bp, respectively. The value entered in the ‘Fail’
field must always be less than the ‘Pass’ field.
Minimum and maximum values allowed by software for Trace
Score are 1 and 60, respectively. The value entered in the ‘Fail’
field must always be less than the ‘Pass’ field.
3. Enter a Protocol ID, and then check the “Use Mixed Base Identification” box on the ‘Mixed-
Bases Setting’ tab, if desired, followed by the Secondary Peak Height Threshold value
(Figure 121).
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Figure 121. ‘New Basecalling Protocol’ screen.

4. Select the ‘Clear Range First bp–Last bp’ tab to reveal the options for setting the first and
last base to consider for analysis (Figure 122).
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Figure 122. ‘Clear Range First bp–Last bp’ tab.
5. Check the “Use Clear Range” box to activate the buttons for choosing the setting for first
and last base (Figure 123). When this is enabled, the first bp position to be considered for
analysis is set by entering this value in the ‘First bp’ field. The default 3´ base setting is Last
bp (e.g., if set to 700bp, any bases after the base pair number 700 will not be analyzed).
Enter the desired values to specify the first and last bases of the sequence to consider for
analysis.
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Figure 123. ‘Use Clear Range’: Last bp view.

6. Select Bases to trim from 3´ end. When this is enabled, the first bp position to be
considered for analysis is set by entering this value in the ‘First bp’ field. The number of
bases to trim from the 3´ end of the sequence is entered into the ‘bp’ field (Figure 124).
Under this setting the last base considered for analysis would depend on the length of
sequence obtained.
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Figure 124. ‘Use Clear Range’: Bases to trim from 3´ end view.
7. Alternatively, the Clear range can be defined by quality value by selecting the “Clear Range
Quality Value” tab and checking the “Use Quality Values” box (Figure 125). In the ‘fewer
than’ field, enter the number of bases that can have a QV lower than that specified in the
‘have QVs less than’ field over a window size specified in the ‘bases out of’ field. For
example, fewer than 4 bases out of a window size of 30 bases can have QVs less than 20
(equivalent to no more than 4 bases over a window size of 30 bases can have a QV less
than 20).
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Figure 125. ‘Clear Range Quality Value’ tab.

8. Select the ‘Sequencing Quality’ tab to reveal the default settings for minimum passing and
maximum failing CRL, QV20+ and Trace Score values (Figure 126). Select which
parameters to use for assessing sequencing quality by checking the appropriate box to the
left of the CRL, QV20+ and Trace Score parameters.
Notes:
1. Suspect CRL, QV20+ and Trace Score value ranges are defined by the minimum
passing and maximum failing CRL, QV20+ and Trace Score values entered.
2. It is not a requirement to select all three sequencing quality parameters. Any one or
two parameters may be selected as well as all three.
Figure 126. ‘Sequencing Quality’ tab. 15880TA
9. Select Save to save the new basecalling protocol, close out of the ‘New Basecalling
Protocol’ screen and return to the ‘Basecalling Protocol List’ screen.
7.2.3 Creating a New Sizecalling Protocol

1. Select Sizecalling Protocols in the ‘New & Edit Protocols’ screen (Figure 117). This opens
the ‘Sizecalling Protocol List’ screen (Figure 127).
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Figure 127. ‘Sizecalling Protocol List’ screen.

2. Select Create in the footer to open the ‘New Sizecalling Protocol’ screen (Figure 128).
There are five tabs in the ‘New Sizecalling Protocol’ screen.
Tab Description
Size Standard Defines the size standard (Figure 129) to use in the sizecalling
protocol and specifies which peaks within the size standard are
used by the sizecalling protocol when calculating sizing quality (SQ)
and electrophoresis quality (EQ). See ‘Result’ Tab in Section 5.7 for
definition of SQ and EQ.
Note: Size standard selected must match that used with samples.
Analysis Range Defines the range in scan numbers/data points from which to process
the data for peak detection.
• Full: Analyzes the entire range from beginning to end of the
collection process, including the primer peak (Figure 130).
• Partial: Allows the user to define the start and end points of the
analysis range in scan number/data points using the fields in the
‘Analysis Range’ tab (Figure 131). The data point range allowed by
software for Start Point and Stop Point is 1 to 32767. The numerical
value for Start Point must always be lower than the numerical value
entered for Stop Point (Figure 131).
Note: Data points outside of the specified analysis range are not
analyzed. Therefore, all of the size standard peaks expected for the
Sizecalling Protocol used must fall within the start and stop points
selected when choosing partial range; otherwise, a failing size quality
will be obtained.
Peak Amplitude Defines the minimum RFU value at which to size and call a peak.
Threshold Peaks below this threshold will not be called, but peaks below the
threshold will still be displayed (range allowed by software is 1RFU to
30,000RFU) (Figure 132). A threshold must be set for the dye channel
used for the size standard. Peaks in the size standard must exceed the
peak amplitude threshold value set in the Sizecalling Protocol in order
for that peak to be considered in the sizecalling algorithm. If a peak or
peaks in the size standard fall below the peak amplitude threshold, it
may result in a reduced SQ and EQ value for that sample. Thresholds
are generally set to be the same as those used for secondary analysis.
Size Quality Defines the SQ values for passing and failing SQ data. Sizing data that
fall between these values will be flagged as “Suspect” (data should
be manually reviewed in ‘Result’ tab to determine whether or not it
is acceptable to the user or requires reinjection). See ‘Results’ Tab in
Section 5.7 for definition of SQ.
Note: Default values are supplied when creating a new sizecalling
protocol but may be edited by the user. The SQ range allowed by the
software is 0.001 to 1. The numerical value for ‘Fail’ must always be
lower than the numerical value entered for ‘Pass’ (Figure 133).

Tab Description
Electrophoresis Defines the EQ values (in bp) for passing and failing data. Sizing data
Quality that fall between these values will be flagged as ‘Suspect’ (data should
be manually reviewed in ‘Result’ tab to determine whether or not it is
acceptable to the user or requires reinjection).
See ‘Result’ Tab in Section 5.7 for definition of EQ.
Note: Default values are supplied when creating a new sizecalling
protocol but may be edited by the user. The EQ range allowed by the
software is 1 to 1,000. The numerical value for Fail must always be
lower than the numerical value entered for Pass (Figure 134).
3. Enter a Protocol ID, and then select a pre-existing Size Standard Protocol from the
drop-down list in the ‘Size Standard’ tab (Figure 128).
4. Select Detail to review the parameters of the selected Size Standard protocol (Figure 129).
Select Close to return to the ‘New Sizecalling Protocol’ screen.
Note: To edit a Size Standard protocol, see Section 7.3.1.
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Figure 128. ‘New Sizecalling Protocol’ screen.

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Figure 129. ‘Size Standard Protocol Details’ from ‘New Sizecalling Protocol’ screen.

5. Select the ‘Analysis Range’ tab to reveal the Analysis Range (Figure 130).
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Figure 130. Full ‘Analysis Range’ tab.
6. The default setting is full range. Partial range analysis can be enabled by selecting Partial,
at which time you are prompted to enter values in bases for the start and stop points for
partial range analysis (Figure 131). Enter a Start Point, in data points, after the primer peak
and before the first required size standard peak. Enter a Stop Point after the last required
size standard fragment. View raw data from previous runs (see Section 6.1) to determine
the appropriate start and stop points.
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Figure 131. Partial ‘Analysis Range’ view.

7. Select the ‘Peak Amplitude’ tab to reveal the options for setting the size standard peak
amplitude thresholds (Figure 132).
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Figure 132. ‘Peak Amplitude’ tab.
8. Enter a Peak Amplitude Threshold value for the dye channel that contains the size
standard. A Peak Amplitude Threshold value must be set for the dye channel that contains
the size standard in order for the sizing quality (SQ) and electrophoresis quality (EQ) to be
determined.
Note: Peaks that fall below the peak amplitude thresholds will still be present and available
for analysis in secondary analysis software.
9. Select the ‘Size Quality’ tab to reveal the default settings for minimum passing and
maximum failing SQ values (Figure 133). These parameters can be changed when creating
a new size calling protocol.
Note: Suspect SQ value range is defined by the minimum passing and maximum failing SQ
values entered.
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Figure 133. ‘Size Quality’ tab.

10. Select the ‘Electrophoresis Quality’ tab to reveal the default settings for minimum passing
and maximum failing EQ values (Figure 134). These parameters can be changed when
creating a new sizecalling protocol.
Note: Suspect EQ value range is defined by the minimum passing and maximum failing EQ
values entered.
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Figure 134. ‘Electrophoresis Quality’ tab.
11. Select Save to save the new sizecalling protocol, close out of the ‘New Sizecalling Protocol’
screen and return to the ‘Sizecalling Protocol List’ screen.

7.2.4 Creating a New Size Standard

Note: A new size standard protocol must be created for use with any new dye set that was
created using the Custom Dye Template (see Section 7.2.6). This new size standard protocol
must be in the same dye channel as that identified for the size standard in the newly created dye
set.
1. Select Size Standard Protocols in the ‘New & Edit Protocols’ screen (Figure 117). This
opens the ‘Size Standard Protocol List’ screen (Figure 135).
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Figure 135. ‘Size Standard Protocol List’ screen.
2. Select Create in the footer of the ‘Size Standard Protocol List’ screen to open the ‘New Size
Standard Protocol’ screen.
3. Enter a unique Size Standard ID, and then select either Red or Orange from the drop-down
list for Dye Color (Figure 136). 18164TA
Figure 136. ‘New Size Standard Protocol’ screen.

4. Select the grid area of the ‘Size Standard Definition’ table (Figure 137).
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Figure 137. ‘New Size Standard Protocol’ screen.
5. A pop-up window will be displayed allowing the user to enter the size for the size standards
(Figure 138). Each value needs to be separated with a comma (,). Select OK to close the
window.
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Figure 138. ‘Size Standard Definition’ screen.
Note: The Size Standard Protocol must have a minimum of four peaks defined. Non-
uniform intervals between the size standard fragments are necessary. Uniform intervals
between the size standard fragments may cause the software to misidentify the sample
and noise peaks. For example:
Uniform intervals: 20, 40, 60, 80 bp (not recommended)
Non-uniform intervals: 20, 40, 80, 140 bp (recommended)

6. Confirm the sizes of the standards displayed on the ‘New Size Standard Protocol’ screen
and select Save (Figure 139).
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Figure 139. ‘Size Standard Definition’ screen.
7. A confirmation message window will be displayed. Select Yes to confirm the changes
7.2.5 Creating a New Assay

1. Select Assay in the ‘New & Edit Protocols’ screen (Figure 117). This opens the ‘Assay List’
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Figure 140. ‘Assay List’ screen.

2. Select Create in the footer to open the ‘New Assay’ screen (Figure 141).
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Figure 141. ‘New Assay’ screen.
3. The ‘New Assay’ screen displays the detailed parameters of the protocol.
Parameter Information
Protocol ID Defines the protocol name.
Application Type Defines whether the protocol is for Sequencing or Fragment
analysis.
Polymer Type Drop-down box allows you to select Polymer4 or Polymer7.1
Dye Set Drop-down box allows you to select the appropriate dye set for
the chemistry being run.
Instrument Protocol Specifies the Instrument Protocol to be applied during data
collection.
Edit opens the Edit Instrument Protocol screen (see Section
7.3.2).
Analysis Protocol Specifies the Analysis Protocol to be appplied to the collected
data:
• Basecalling Protocol for Sequencing analysis.
• Sizecalling Protocol for Fragment analysis.
Edit opens the Edit Analysis Protocol screen (see Section 7.3.2).
1
Only Polymer7 can be chosen for Sequencing analysis. Polymer4 is not allowed for sequencing analysis.
Note: Edits made to the Instrument or Analysis Protocol from the ‘Edit Assay’ screen do
not change the parameters of those protocols stored in the library. Changes are only stored
with the specific assay.
4. Enter a Protocol ID, and then select or enter the appropriate settings for the new assay.
5. Select Save to close the ‘New Assay’ screen and return to the ‘Assay List’ screen.

7.2.6 Creating a New Dye Set

A dye set for an assay can be selected from a preloaded Dye Set or by creating one. Dye sets
may be created by selecting a dye set template based on a preloaded dye set (in which case,
only Condition Number and Quality Value may be changed) or the Custom Dye Template. The
Custom Dye Template does not have optimized binning but allows freedom to choose the
following:
• Dye selection for spectral calibration
• Order of dyes in the spectral calibration standard
• If all or a subset of the dyes used in the spectral calibration are used in the samples run
with that dye set.
• Condition Number and Quality Value
• Dye channel that will be used for size standard in samples run with that dye set.
Note: Custom matrix standards should meet all the following criteria:
• Size range: 60–300bp
• Peak height: ≥500RFU
• Peak height ratio (min/max): ≥¼ (or 25%) (For example, the peak height ratio is 25% when
the maximum peak height is 4,000RFU and the minimum peak height is 1,000RFU).
Notes:
a. A preloaded dye set can be duplicated by creating a new dye set using that preloaded dye
set as the template. A preloaded dye set cannot be duplicated by editing a preloaded dye
set.
b. Fragment migration time is reduced by low ambient temperature and/or aged polymer
(polymer close to its expiration date and/or that has been on the instrument for almost
14 days). If using large spectral calibration fragments (e.g., close to 300bp limit), not all
fragments will be detected when run under these conditions. This will result in failing
spectral calibration.

1. Select Dye Set in the ‘New & Edit Protocols’ screen (Figure 117). This opens the ‘Dye Set
List’ screen (Figure 142).
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Figure 142. ‘Dye Set List’ screen.
2. Select Create in the footer of the ‘Dye Set List’ screen to open the ‘New Dye Set’ screen.
3. Enter a Dye Set ID and select the appropriate Application and Dye Set Template (Figure
143). Select Edit.
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Figure 143. ‘New Dye Set’ screen.
Note: When the Custom Dye Template is selected from the ‘Dye Set Template’ drop-down
box, you can custom select dyes and the dye detection order. When you select an existing
dye set template, you can only edit the Condition Number and Quality Value.

4. Using the ‘Dye Color’ drop-down box, assign a dye color for the Size Standard (Figure 144).
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Figure 144. ‘Edit Dye Condition’ screen.
Note: When creating a new dye set using the Custom Dye Template, a new custom size
standard must be created (see Section 7.2.4) in the dye channel selected for the size
standard. Using one of the preloaded size standards with a new dye set created using the
Custom Dye Template is not possible, even if the preloaded size standard is in the same
dye channel as that selected for the size standard in the new dye set. Alternatively, if a new
dye set is created using one of the preloaded dye set templates (e.g., Promega 5-Dye
Template), then using a preloaded size standard (e.g., WEN ILS can be used with Promega
5-Dye) is possible as well as a new custom size standard (in the dye channel selected for
the size standard in the new dye set).
5. Select the dyes used for Spectral Calibration on the Matrix Dyes row. Select the dyes used
for samples on the Sample Dyes row (Figure 145).
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Figure 145. Selecting the dyes in the ‘Edit Dye Condition’ screen.
Note: The dye color selected for the Size Standard must be selected for the Matrix Dyes
and Sample Dyes. All or a subset of the dyes selected for the Matrix Dyes may be selected
as Sample Dyes.

6. Configure the dye order in Calibration Peak Order. This dye order represents the order that
the software expects the different dye labeled fragments to pass the detector (Figure 146).
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Figure 146. Configuring the dye detection order in the ‘Edit Dye Condition’ screen.
7. An example of the electrophergram image matching the dye order described in Figure 146
is shown in Figure 147.
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Figure 147. Dye order detected in Spectral Calibration.

8. Enter the values for Condition Number and Quality Value (Figure 148). Select Apply.
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Figure 148. Adding Condition Number and Quality Values to the ‘Edit Dye Condition’ screen.
The following Table lists the Preloaded dye sets, Condition Numbers and Quality Values for
Dye Sets.
Condition Number Quality Value

Application Template Upper Limit Lower Limit
Fragment Promega 4-dye 8.5 0.95
Fragment AB 5-dye 13.5 0.95
Fragment AB 6-dye 8 0.95
Fragment Qiagen 5-dye 20 0.95
Fragment Qiagen 6-dye 13.5 0.95
Fragment Custom Dye 20 0.80
Sequencing AB 4-dye sequencing 5.5 0.95
Sequencing Promega 4-dye sequencing 5.5 0.95

9. Confirm that the New Dye Set screen reflects the essential information for the custom dye
set (Figure 149). Select Save.
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Figure 149. Saving the custom dye set in the ‘New Dye Set’ screen.
7.3 Editing Protocols, Assays and Dye Sets

Select New & Edit Protocols on the ‘Main Menu’ screen (Figure 9) to access the ‘New &
Edit Protocols’ screen (Figure 117). Instrument, Basecalling, Sizecalling and Size Standard
protocols, Assays and Dye Sets can be accessed and edited from here.
7.3.1 Editing Size Standard Protocol

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Figure 150. ‘Size Standard Protocol List’ screen.

2. Locate the desired Size Standard protocol in the list using scroll buttons on the right side of
the list. Select the size standard you want to edit on the ‘Size Standard Protocol List’ screen
(Figure 150). This will activate Edit and Delete in the footer (Figure 151).
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Figure 151. ‘Size Standard Protocol List’ screen with selected Size Standard.
3. Select Edit in the footer to open the ‘Edit Size Standard Protocol’ screen (Figure 152).
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Figure 152. ‘Edit Size Standard Protocol’ screen.

4. Specific fragment sizes that are enabled for use by the software are indicated in orange or
red, depending on the dye channel in which the size standard is located, whereas fragment
sizes that are disabled for use are grayed out. The controls on the ‘Edit Size Standard
Protocol’ screen are as follows.
Setting Description
Size Standard Defines the size standard name
Dye Color Specifies the dye channel containing the size standard
fragments (not editable).
Size Standard Definition Defines the fragment sizes to be used for creating a sizing
curve (Orange or Red shading indicates the size is to be used.
Gray shading indicates the size will not be used).
Individual sizes can be selected or deselected by selecting the
corresponding size on the screen.
Use All —selects all listed sizes for use in sizecalling.
5. Make the desired changes to the Size Standard Protocol by selecting the specific fragment
size you wish to disable (grayed out) or use (orange or red), and then select Save in the
footer to save the changes and overwrite the existing protocol (if it is not locked), or select
Save As to save as a new protocol.
6. Enter a Size Standard Protocol name in the Size Standard name field that opens after
selecting Save As. A keypad will become active on the touch screen. Alternatively, the new
Size Standard Protocol name can be entered using a traditional keyboard if one is
connected to the Spectrum Compact CE System. Select OK to exit. A warning window
asking “Are you sure you want to create a new Protocol” appears. Selecting Yes completes
the ‘Save As’ function and takes you back to the ‘Size Standard Protocol List’ screen.
Selecting No closes the ‘Save As’ function and takes you back to the ‘Edit Size Standard
Protocol’ screen.
7.3.2 Editing Instrument, Sizecalling and Basecalling Protocols, Assays and Dye Sets
Editing existing Instrument, Sizecalling and Basecalling protocols, Assays and Dye Sets is as
stated in Section 7.2, and then referencing the appropriate section for creating new protocols
and assays as shown.
Edit Screen Creating Assays and Protocol Section

Edit Instrument Protocol 7.2.1 Creating a New Instrument Protocol
Edit Basecalling Protocol 7.2.2 Creating a New Basecalling Protocol
Edit Sizecalling Protocol 7.2.3 Creating a New Sizecalling Protocol
Edit Size Standard Protocol 7.2.4 Creating a New Size Standard Protocol
Edit Assay 7.2.5 Creating a New Assay
Edit Dye Sets 7.2.6 Creating a New Dye Set

7.4 Deleting Protocols, Assays and Dye Sets

1. Select New & Edit Protocols on the ‘Main Menu’ screen (Figure 9) to access the ‘New &
Edit Protocols’ screen (Figure 117). Instrument, Basecalling, Sizecalling and Size Standard
protocols, Assays and Dye Sets can be accessed and deleted from here after touching the
appropriate section. Below is an example using the ‘Size Standard Protocol’ screen.
Note: Preloaded protocols and assays cannot be deleted.
3. Locate the desired Size Standard protocol in the list using scroll buttons on the right side of
the list. Select the size standard you wish to delete on the ‘Size Standard Protocol List’
screen (Figure 150). This will activate Edit and Delete in the footer (Figure 151).
4. Select Delete. A warning window asking “Are you sure you want to delete the protocol?” will
appear. Selecting Yes deletes the protocol and takes you back to the ‘Size Standard
Protocol List’ screen. Selecting No closes the window and takes you back to the ‘Size
Standard Protocol List’ screen without deleting the protocol.
7.5 Exporting and Importing Protocols and Assays

Instrument, Basecalling, Sizecalling and Size Standard protocols and Assays can be exported
from one Spectrum Compact CE System and imported into another via a USB drive. All
protocols are exported together in one .xml file. An example for exporting and importing
Assays is shown in Sections 7.5.1 and 7.5.2.
Notes:
1. Only user-defined protocols can be exported from one instrument and imported into
another.
2. Dye sets cannot be exported from one instrument to another.

7.5.1 Exporting Protocols and Assays

1. Select Export All Protocols on the ‘Main Menu’ screen (Figure 9) to access the ‘Export All
Protocols’ screen (Figure 153). Enter a File Name for the exported protocols file by
selecting the File Name field. This opens the ‘File Name’ window, and a keypad will become
active on the touch screen. Alternatively, the File Name can be entered using a traditional
keyboard if one is connected to the Spectrum Compact CE System. Enter the appropriate
File Name, and then select OK to exit and return to the ‘Export All Protocols’ screen.
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Figure 153. ‘Export All Protocols’ screen.
2. Insert a USB drive into the USB port in the front of the instrument.
3. Select Export All on the ‘Export All Protocols’ screen (Figure 153). A confirmation window
will appear asking “Are you sure you want to export the protocols to the USB Device?”
Select Yes to export the file, or select No to cancel out of the export process.
4. After completion of the export an information window will appear stating “Export
completed successfully”. Select OK followed by USB icon in the header before removing
the USB drive from the storage USB port.
7.5.2 Importing Protocols and Assays

1. Select Import Protocols on the ‘Main Menu’ screen (Figure 9) to access the ‘Import
Protocols’ screen (Figure 154).
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Figure 154. ‘Import Protocols’ screen.

2. Insert a USB drive containing the exported protocols file (see Section 7.5.1) into the USB
port in the front of the instrument.
3. Select the appropriate protocol type on the ‘Import Protocols’ screen (Figure 154). This
displays the ‘Assay List’ screen (Figure 155).
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Figure 155. ‘Assay List’ screen.
4. Locate the desired protocol in the list using scroll buttons on the right side of the list. The
filter and sort buttons may be used to aid in locating the protocol.
5. When the protocol is located, select it from the list, and then select Import in the footer.
Note: While it is possible to view the details for the individual assay/protocol selected in
Step 5 by selecting View, it cannot be edited from this path. To edit an imported protocol,
follow the steps in Section 7.3 after the import is complete.
6. If an individual assay/protocol shares the same name as an existing protocol, a
confirmation window will appear asking “Are you sure you want to overwrite?” Select Yes to
proceed or Cancel to exit without importing.
7. Selecting No opens a ‘Protocol ID’ window and a keypad on the touch screen that allows
the assay/protocol to be renamed prior to import. Alternatively, the new Protocol ID can be
entered using a traditional keyboard if one is connected to the Spectrum Compact CE
System. Enter the appropriate Protocol ID, and then select OK. A confirmation window will
appear asking “Are you sure you want to import a new protocol?” Select Yes to proceed or
No to exit without importing.
8. Alternatively, select Import All to import all the assays. A confirmation window will appear
asking “Are you sure you want to import all protocols into the instrument?” Protocols that
cannot be overwritten and protocols with invalid settings will skip import. Select No to exit
the import and Yes to proceed with the import.
9. If an individual assay/protocol already exists, a confirmation window will appear asking
“Are you sure you want to overwrite?” Select OK to overwrite or Skip to go to the next
assay/protocol. Select Cancel to exit.

7.5.3 Chemistry Kit Add-on

The Chemistry Kit Add-on function allows the user to add Assays for new Chemistry Kits in the
future.
1. Insert a USB drive that contains the Chemistry Add-on protocols in a sub-folder called
ChemistryKit into the USB port on the front of the instrument.
2. Select Import Protocols on the Main Screen (Figure 156).
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Figure 156. ‘Main’ screen.
3. Select Chemistry Kit to import the desired protocol (Figure 157). After this step, follow the
procedure described in Section 7.5.2 Importing Protocols and Assays.
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Figure 157. ‘Import Protocols’ screen.

Managing Instrument Settings 8
Instrument settings are accessed through Settings, located in the footer on the ‘Main
Menu’ screen (Figure 9) of the Spectrum Compact Control Software when logged in as an
administrator (this button is not visible when logged in as a user). There are six types of
instrument settings available in the Settings screen (Figure 158):
1. System Settings
2. Network Settings
3. Security Settings
4. User Account
5. Backup Settings
6. File Name Convention
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Figure 158. ‘Settings’ screen.
When the security level is set to High (Section 8.3), instrument settings are only accessible
when logged in as an administrator. They are not accessible when logged in as a user. When
security level is set to Normal (Section 8.3), all users have access to all instrument settings, but
it is not possible to edit user rights as described in Section 8.3.1.
Note: When security level is set to Normal (Section 8.3), an additional button is visible on the
‘Settings’ screen called Service. This setting is for use by service engineers.

Managing Instrument Settings
8.1 System Settings

The System Settings allow the user to edit the instrument name and to set the display of the
decimal separator as a period (.) or a comma (,). The default setting is a period.
1. Select System Settings in the ‘Settings’ screen (Figure 158) to open the ‘System Settings’
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Figure 159. ‘System Settings’ screen.
2. Enter an instrument name in the provided field using up to 15 characters. Only single-byte
alphanumeric characters and hyphens can be used.
3. Select “comma (,)” in the Decimal Separator drop-down box to change the default display
of the setting from period to comma.
4. Select Apply in the footer to save the name and apply it to the System Settings.
5. A Confirmation message followed by an Information message will be displayed (Figure 160).
Select OK. Restart the system to make the changes take effect.
Note: When changing the Instrument Name, make sure the LAN cable is connected before
you restart the system to enable the Remote Access function.
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Figure 160. ‘Information’ screen.

8.2 Network Settings

Network Settings allows the user to edit the network settings for the instrument. There are two
methods for connecting the instrument to an external computer.
1. Direct connection to external computer

2. Connection via Local Area Network (LAN)
8.2.1 Direct Connection to Computer

1. Connect an Ethernet cord from the instrument’s Ethernet connection to the Ethernet
connection of an external computer’s network interface card.
2. Select Network Settings in the ‘Settings’ screen (Figure 158) to open the ‘Network Settings’
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Figure 161. ‘Network Settings’ screen.
3. The ‘Network Settings’ screen displays the instrument’s settings for the network. For the
instrument and external computer to successfully communicate, the following network
information is required.
Setting Description
Use DHCP Ensure that this box is unchecked to enable the network settings
fields if connecting directly to a computer [Default = Unchecked]
IP Address The IP address assigned to the instrument
Sub Net Mask The sub net mask assigned to the instrument, which should be
the same as the external computer’s sub net mask
[Default = 255.255.255.0]
Default Gateway The IP address of the default gateway [Default = 0.0.0.0]
4. Select Apply in the footer to apply and save the Network Settings.
Note: Refer to your IT administrator for configuring network settings on the Spectrum
Compact CE System and external computer if applicable.

8.2.2 Connection via LAN

1. Connect an Ethernet cord from the instrument’s Ethernet connection in the rear of the
instrument to your network.
2. Select Network Settings in the ‘Settings’ screen (Figure 158) to open the ‘Network Settings’
3. Contact your IT administrator for the proper network information and configuration (see
Section 8.2.1).
4. Select Apply in the footer to apply and save the Network Settings.
8.3 Security Settings

Security Settings allows the user to edit the instrument’s security settings.
Note: The security level setting will affect the ability to view and edit the protocol settings (see
Section 7).
1. Select Security Settings in the ‘Settings’ screen (Figure 158) to open the ‘Security Settings’
screen. The ‘Security Settings’ screen is different for High (Figure 162) and Normal
(Figure 163) security levels.
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Figure 162. High-level ‘Security Settings’ screen.

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Figure 163. Normal-level ‘Security Settings’ screen.
2. Select the desired security level.
Security Level Available Security Settings

Normal None—all users are logged in as Administrator. Password, screen lock
and login functions are disabled.
High All—password, screen lock and login functions are enabled.
If High is selected, select the desired settings for Password expiration and screen lock.
High-Level Settings Description

Password Expiration Check box to activate password expiration.
Select the number of days before expiration (10–180) from the
drop-down list.
Screen Lock Select the number of minutes (1–60) of idle time to engage the
screen lock.
3. Select Apply in the footer to apply and save the Security Setting.
Note: User Rights in the bottom right corner provides a shortcut to the User Rights setting
(see Section 8.3.1).
4. When switching between Normal and High security levels, after selecting Apply a
confirmation window will appear asking “Are you sure you want to change the system
settings?”. Selecting Yes brings up an information window asking you to “Please shut down
and restart the system”. (See Section 10 for instructions on shutting down the system).
Selecting No closes out the confirmation window and takes you back to the ‘Security
Settings’ screen.

8.3.1 User Rights

Under the High security level, the User Rights setting allows the administrator to manage the
access rights assigned to the User accounts (see Section 8.4). Changes made to user rights
affect all User accounts.
Notes:
a. Changes made to user rights do not affect administrators.
b. Access rights granted to User accounts by the administrator only applies when the
security level is High. With Normal security level selected, all users are treated as
administrators and User Rights is not active.
c. Changes made to user rights by the administrator require that the administrator logs
out and shuts down and restarts the system after the change, and before a user logs
in. Changes to user rights will not be applied if the system is not shut down and
restarted after the administrator logs out.
1. Select User Rights in the bottom right corner of the ‘Security Settings’ screen under the
High security level (Figure 162) to open the ‘User Rights’ screen (Figure 164).
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Figure 164. ‘User Rights’ screen.
2. There are seven rights that can be assigned to the User, five of which pertain to Protocols:
Right Description
Protocols Allows management of protocols. Options include allowing users to
Create, Edit, Delete, Import or Export protocols.
Calibrations Allows performance of calibrations on the instrument.
System Test Allows access to the System Test Results.
Notes:
a. System Test should only be performed by a Promega service engineer.
b. Assays and protocols created under high-security settings by a user without
administrative rights are locked from other users without administrative rights but not
from users with administrative rights.
3. Select or enter the appropriate settings for the User.

4. Select Apply in the footer to apply and save the settings to the User Rights.
5. Log out as administrator, and then shut down and restart the system (see Section 10 for
instructions on shutting down the system and Section 2.1 for starting the system) before
logging in as a user. Shutdown and restart of the system is required for the changes in user
rights to be enabled.
8.4 User Accounts

The User Account setting allows the user to create, edit or delete the user accounts
associated with the instrument. New accounts may be created by the administrator under
the High security level. Anyone may create a new account under the Normal security level.
The User Rights function is disabled under Normal security level as all users are considered
administrators (see Section 8.3.1).
Note: If User level is chosen for a new user account, the user’s available functions will depend
on the user rights selected in Section 8.3.1. A comparison of User and Administrator rights
under High security is shown in the following table.
Function User Administrator

Performing Run Available Available
Creating New Protocols Depends on user’s rights (Section 8.3.1) Available
Editing Protocols Depends on user’s rights (Section 8.3.1) Available
Deleting Protocols Depends on user’s rights (Section 8.3.1) Available
Importing Protocols Depends on user’s rights (Section 8.3.1) Available
Exporting Protocols Depends on user’s rights (Section 8.3.1) Available
Calibration Depends on user’s rights (Section 8.3.1) Available
System Tests Depends on user’s rights (Section 8.3.1) Available
Backup Unavailable Available
Software Update Unavailable Available
Miscellaneous Settings1 Unavailable Available
Consumables Exchange Available Available
Reviewing Result Available Available
System Log Available Available
1
Miscellaneous Setttings refers to:
• System Settings
• Network Settings
• Security Settings
• User Account
• User Rights
• File Name Conventions
• Adjusting Date and Time

8.4.1 Creating a New User Account

1. Select User Account in the ‘Settings’ screen (Figure 158) to open the ‘User Account’ screen
(Figure 165).
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Figure 165. ‘User Account’ screen.
2. Select Create in the footer to open the ‘New User Account’ screen (Figure 166).
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Figure 166. ‘New User Account’ screen. The ‘New User Account’ screen displays the available user settings.
Note: Items indicated with an asterisk are required.

Setting Description
User ID Defines the login ID. Unacceptable characters for User ID are
#%&{}\<>*?/$!’”:@+`|= and space
User Level User—selecting this level allows customization of user rights (see
Section 8.3.1)
Administrator
Description Defines the user’s name. Unacceptable characters for Description
are #%&{}\<>*?/$!’”:@+`|=
Password Defines the user’s password for login
Re-enter Password Confirms entered password
Network Access Defines user’s ability to access instrument via Spectrum Compact
Remote Access Software
Spectrum Compact CE System password requirements are as follows:
Password Parameters Description

Minimum length 6 characters
Allowable characters1 a–z, A–Z, 0–9, ~^()=$@!#%&’-+_[ ]{ }
Suggested character combinations [a–z, A–Z] or [a–z, 0–9] or [A–Z, 0–9]
or [a–z, A–Z, 0–9]
Not allowed Cannot be same as User ID
Cannot be same as Description
Cannot have been used for any of the three
previous passwords
1
Same as Windows® file name restrictions
3. Select or enter the appropriate settings for the user.

4. Select Apply in the footer to apply and save the settings to the user account.
8.4.2 Editing a User Account

(Figure 165).
2. Locate the desired user account using the scroll buttons on the right side of the list. The
sort buttons (ID and Level) at the top of the list can be used to aid in locating the user
account.

3. Select the user account from the list, and then select Edit in the footer to open the ‘Edit
User Account’ screen (Figure 167).
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Figure 167. ‘Edit User Account’ screen.
4. Make the desired changes to the user account, and then select Apply in the footer to apply
and save the changes.
8.4.3 Deleting a User Account

(Figure 165).
2. Locate the desired user account using the scroll buttons on the right side of the list. The sort
buttons (ID and Level) at the top of the list can be used to aid in locating the user account.
3. Select the user account from the list, and then select Delete in the footer.
4. Select Yes in the confirmation window to delete the account.
Note: Administrators can delete user accounts at the User and Administrator level, but it is
not possible to delete a user that is currently logged in.
8.5 Backup Settings

System backup occurs automatically when the Spectrum Compact CE System is shutdown if
this function is enabled.
1. Select Backup Settings in the ‘Settings’ screen (Figure 143) to open the ‘Backup Settings’
2. Select Enable to activate the system backup or Disable to deactivate system backup, and
then choose Apply (Figure 168).
3. After selecting Apply, a confirmation window will appear asking “Are you sure you want to
change system settings?”. Select Yes, to accept the change and No to revert to previous
settings.

4. With System Backup enabled, the system is automatically backed up to a separate drive
within the Spectrum Compact System every time the instrument is shutdown. System
recovery can only be performed by a service engineer.
Note: Log files, IP addresses and instrument name are not included in the system backup.
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Figure 168. ‘Backup Settings’ screen.
8.6 File Name Conventions

File Name Conventions allows the user to edit global file name settings for either fragment or
sequencing file names (i.e., fsa files created for fragment analysis and ab1 files created for
sequencing analysis).
1. Select File Name Conventions in the ‘Settings’ screen (Figure 158).

2. Settings for Sequencing and Fragment analyses are displayed (Figure 169). Attributes
enclosed within <> are separated by delimiters (_). Users can preview or edit file name
conventions on this screen.

3. Select Edit to change File Name Conventions (Figure 169).
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Figure 169. ‘File Name Conventions’ screen.
4. Select the row you intend to edit from the ‘File Name Conventions List’ screen (Figure 170).
Select Edit.
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Figure 170. ‘File Name Conventions List’ screen.

The following table explains the features and rules for editing the information on the ‘File Name
Conventions List’ screen.
Used Allows the user to select an attribute. An Order Number is

automatically assigned to the attribute.
Order (▲ and ▼ buttons) Allows the user to set the order of the attribute displayed in
the file name.
Attribute Displays the set attribute used in the file name. Table 1-2 lists
the rules for creating attributes.
Delimiter Allows the user to set a delimiter displayed in the file name.
Acceptable characters for delimiters are “- “, “.” or “_”. It is not
mandatory to specify a delimiter.
Custom Text An arbitrary string of up to 30 alphanumeric characters can
be entered for this attribute. Unacceptable characters such as
#%&{}\<>*?/$!’”:@+`|= and space cannot be used.
Reset Resets settings to initial settings.
Refresh Sorts the items in the ascending order of set Order numbers.
Preview Allows the user to view the edited attributes.

The following table explains the Rules for characters when setting Attributes.
Number of Characters
Attribute Description Minimum Maximum
Assay ID ID of the assay used in the injection 1 40
Capillary Number Capillary Number (1 to 4) 1 1
Custom Text An arbitrary character string can be 0 30
set.
Date of Run Start date of the run (YYYYMMDD) 8 8
Injection Number Injection Number (1 to 24) 2 2
Date and Time of Injection Date and time when the injection 14 14
started (YYYYMMDDHHMMSS, in
24-hour notation)
Instrument Name Name of the instrument that 1 15
executed the run
Polymer Type Polymer Type (Polymer4/Polymer7) 8 8
Run ID Run ID 1 30
Sample Name Sample Name 1 30
Sample Type Sample type 6 15
Strip ID Strip ID used in the injection 1 30
Unique Time Stamp Specific time stamp (in milliseconds) 13 13
Integer
User ID User ID 0 28
Well Position Well position of the sample 2 2
(A1 to A8, B1 to B8, C1 to C8, D1 to
D8)
Note: The file name can consist of up to 180 characters (including the file extension).

5. Select Apply after editing the necessary information for each attribute (Figure 171).
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Figure 171. ‘Attribute Edit’ screen.
Note: You can only edit the Custom Text field when editing the Custom Text attribute.
6. Return to the ‘File Name Conventions List’ screen (Figure 172). Select Apply.
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Figure 172. ‘File Name Conventions List’ screen.
change the File Name Conventions settings?”. Select Yes, to accept the change and No to
revert to previous settings.

8. Select Preview in the ‘File Name Conventions’ screen (Figure 173) to verify the edits made
to the attributes.
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Figure 173. ‘File Name Conventions’ screen.
9. An example of the ‘Preview’ screen is shown in Figure 174.
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Figure 174. ‘Preview’ screen.
8.7 Adjusting Date and Time

When logged in as an Administrator (but not as a User), the date and time can be edited on the
1. Select date and time in the upper right hand corner of the ‘Main Menu’ screen (Figure 9) to
open the ‘Date and Time Settings’ screen (Figure 153).

2. Change year, month, day, hours, and minutes on ‘Date and Time Settings’ screen, then
select Apply (Figure 175).
change date and time?”. Select Yes to accept change and No to revert to previous settings.
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Figure 175. ‘Date and Time Settings’ screen.

Instrument Information 9
9.1 System Information
Instrument information is accessed through About, located in the footer on the ‘Main Menu’
screen (Figure 9) of the Spectrum Compact Control Software. The About function is available
on the ‘About’ screen (Figure 176).
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Figure 176. ‘About’ screen.
Selecting About on the ‘About’ screen (Figure 176) displays the ‘Instrument Information’ screen
(Figure 177), which contains the following instrument information:
1. Instrument Name
2. Serial Number
3. Product Name
4. Hardware Version
5. Instrument Software System Version
6. Remote Access Software Version
7. Instrument Software Checksum
Note: The instrument and remote access software versions can be updated from this screen.

Instrument Information
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Figure 177. ‘Instrument Information’ screen.
9.2 Alarm List

The most recent instrument alarms (up to 200) are logged in the ‘Alarm List’ screen (Figure 178)
of the Spectrum Compact Control Software.
1. Select Alarm, located in the header of the ‘Main Menu’ screen (Figure 9) of the Spectrum
Compact Control Software to access the ‘Alarm List’ screen (Figure 178).
Note: When the instrument is turned off or rebooted, the Alarm List is saved to an alarm
log file. This file can be retrieved from the Alarm Log (see Section 6.4.1).
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Figure 178. ‘Alarm List’ screen.
2. When there is a new alarm, an amber indicator appears on the Alarm icon with a white
number indicating the number of new alarms. When selecting Alarm, the ‘Alarm List’
screen opens (Figure 178). Once you have reviewed the new alarm(s), the indicator on the
Alarm icon goes away.

Instrument Information
3. Select a specific Alarm in the list followed by Details to review the details of that specific
alarm (Figure 179).
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Figure 179. ‘Alarm Detail’ screen.
The ‘Alarm Detail’ screen provides the following information:
Information Description
Date/Time/Code Date and time the alarm occurred and the alarm code
(see Section 11 for error code list)
Type Critical Alarm—a severe condition,
such as instrument malfunction, has
occurred.
Error Alarm—an error preventing
electrophoresis has occurred.
Warning—something needs attention,

but the instrument will continue
operation.
Details Describes what caused the alarm.
Recommended Action Describes the recommended corrective action(s) to
resolve the issue.
4. Check the information displayed in the Details and Recommended Action section of the
‘Alarm Detail’ screen (Figure 179). Perform corrective measures required to address the
information displayed. See Section 11 for a list of error codes and responses.
5. To view information for the previous or next alarm, select Previous or Next, respectively.
6. Select Close to return to the ‘Alarm List’ screen.
Note: Shutting down the Spectrum Compact CE System (see Section 10) clears alarms
from the ‘Alarm List’ screen.

Shutting Down the Instrument 10
There are two levels of shutdown for the Spectrum Compact CE System:
1. Short-term shutdown
2. Long-term shutdown
10.1 Short-Term Shutdown

Short-term shutdown of the instrument, such as during a reboot of the system, can be
performed under both Normal and High security levels.
10.1.1 Normal Security Level Shutdown

1. Select Shutdown in the footer of the ‘Main Menu’ screen (Figure 180) of the Spectrum
Compact Control Software.
15910TA
Figure 180. ‘Main Menu’ screen (Normal security).

Shutting Down the Instrument
2. Wait for the Shutting Down screen to disappear completely and a pointer will appear on the
screen. After the pointer disappears, turn the instrument power switch to the Off position.
18418TA
Figure 181. Shutting Down and pointer display screens.
10.1.2 High Security Level Shutdown

1. Select Logout in the footer of the ‘Main Menu’ screen (Figure 182) of the Spectrum
Compact Control Software. A confirmation window will appear asking “Are you sure you
want to log out?”. Select Yes to proceed to ‘Login’ screen (Figure 183). Select No to return
to the ‘Main Menu’ screen (Figure 182).
15911TA
Figure 182. ‘Main Menu’ screen (High security).

2. Select Shutdown in the ‘Login’ screen (Figure 183).
15912TA
Figure 183. ‘Login’ screen.
3. When a Confirmation message is displayed, touch the Yes button. The following screen is
displayed.
18418TA
Figure 184. Shutting Down and pointer display screens.
4. Wait for the Shutting Down screen to disappear completely and a pointer will appear on the
screen. After the pointer disappears, turn the instrument power switch to the Off position.

10.2 Long-Term Shutdown

The long-term shutdown procedure should be performed if the instrument will be out of use for
more than 2 weeks. To shutdown the instrument for long-term storage, all consumables must
be removed from the instrument.
1. Use the Uninstall wizard in the ‘Installed Capillary Cartridge Information’ screen to remove
the Capillary Cartridge from the instrument (see Section 3.3).
Note: To store the capillary cartridge for use at a later date, fill the capillaries with polymer
by selecting Fill in the wizard. Then fill the capillary anode and cathode covers with
Capillary Preservation Buffer and place them on the cartridge as described in Section 3.3.
Store the uninstalled capillary cartridge upright at ambient temperature.
2. Select Eject in the header on the ‘Main Menu’ screen (Figure 9) of the Spectrum Compact
Control Software to move the autosampler forward to access the consumables housed in
the autosampler.
3. Remove the Spectrum Compact ABC by pressing in on the locking tabs on either side of
the Spectrum Compact ABC and pulling up to detach it from the deck.
Note: Discard opened and used Spectrum Compact ABC. Do not store for later use.
4. Remove the Spectrum Compact CBC by pressing in on the locking tabs on either side of
the Spectrum Compact CBC and pulling up to detach it from the deck.
Note: Discard opened and used Spectrum Compact CBC. Do not store for later use.
5. Remove the Polymer Cartridge by pulling the yellow locking catch to the left and pulling up
on the cartridge (Figure 29). Unexpired Polymer Cartridges may be stored at 4°C for later
use if injections remain.
Note: The on-instrument expiration date will remain the same as it was at first installation
upon reinstallation of the Polymer Cartridge.
6. Remove the sample cartridge by pushing down on the yellow tab on the autosampler deck
that locks the sample cartridge in place and then lifting up on the sample cartridge.
7. Close the front door of the instrument, and wait for the status indicator to stop flashing
amber and turn a steady green.
8. With the consumables and sample cartridge removed, shutdown the instrument software
as described in Section 10.1.

Error Messages 11
The following table is a list of error codes, their meaning and the appropriate response.
Error Code Error Message Message Detail Response

1001 System error Operational unit system Restart the instrument.
(application) error If alarm persists, contact
Technical Service with
alarm code indicated.
1002 Communication error Operational unit Restart the instrument.
communication error If alarm persists, contact
1007 Database access error Database access has Restart the instrument.
failed If alarm persists, contact
1013 Shutdown status error The system has not Confirm that the last run
been properly shut data is saved.
down
Your operation may
have been terminated
1014 File access error File access has failed Restart the instrument.
If alarm persists, contact
1015 Drive access error Drive access has failed Restart the instrument.
1016 Data collection error System encountered an Restart the instrument.
unexpected error while Rerun samples.
collecting the data If alarm persists, contact

Error Messages

1017 Data collection error System encountered an Restart the instrument.
unexpected error while Rerun samples.
collecting the data If alarm persists, contact
1018 Spatial Calibration Instrument door opened Ensure that the instrument
aborted or error occurred while door is closed.
performing Spatial Check the instrument
Calibration conditions.
1019 Spectral Calibration Instrument door opened Ensure that the instrument
aborted or error occurred while door is closed.
performing Spectral Check the instrument
Calibration conditions.
1020 Run aborted Instrument door opened Ensure that the instrument
or error occurred while door is closed.
performing Run Check the instrument
conditions.
1021 System Test aborted Instrument door opened Ensure that the instrument
or error occurred while door is closed.
performing System Test Check the instrument
conditions.
2001 Primary analysis error Timeout occurred Restart the instrument.
during primary analysis Rerun sample.
3003 Software error Script execution error Restart the instrument.
(application) detected If alarm persists, contact
3008 Communication error Ethernet CEU Ethernet
communication error communication error
detected detected.
3030 Instrument power Instrument power Restart the instrument.
supply self-test error supply failed during If alarm persists, contact
initialization Technical Service with
3031 Laser self-test error Laser failed during Restart the instrument.
initialization If alarm persists, contact

Error Messages

3032 CCD camera self-test CCD camera failed Restart the instrument.
error during initialization If alarm persists, contact
3033 Instrument ambient Instrument ambient Restart the instrument.
temperature sensor temperature sensor Check that the ambient
self-test error failed during temperature is in the
initialization allowable range of +15°C
to +30°C (+60°F to + 85°F).
3034 High voltage low Possible moisture Remove any liquid around
current detected in and around the the septa, Cathode Buffer
septa, Cathode Buffer Cartridge, oven and
Cartridge, oven, or the autosampler.
autosampler caused Check the Anode electrode
arcing for damage.
Contact Technical Service
if damage or arcing is
observed.
3035 High voltage self-test High voltage failed Restart the instrument.
error during initialization If alarm persists, contact
3040 Instrument initialization Instrument error Restart the instrument.
failed detected during If alarm persists, contact
initialization Technical Service with
3099 Software error Internal software error Restart the instrument.
(application) detected If alarm persists, contact
3111 Oven temperature Ambient temperature is Ensure that the over door
outside tolerance too high or low is closed properly.
Check that the ambient
temperature is in the
allowable range of +15°C
to +30°C (+60°F to + 85°F).

Error Messages

3112 Oven high temperature Oven temperature Restart the instrument.
error exceeds the upper limit If alarm persists, contact
3115 Oven temperature Oven temperature did Ensure that the over door is
stabilization error not stabilize within the closed properly.
required time Check that the ambient
to +30°C (+60°F to + 85°F).
3120 Oven temperature Oven temperature Restart the instrument.
sensor error sensor has failed If alarm persists, contact
3199 Oven internal Oven internal software Restart the instrument.
processing error error detected If alarm persists, contact
3211 High voltage tolerance High voltage is unstable Check Polymer, Anode,
error and Cathode levels and for
the presence of bubbles.
Check Anode electrode for
damage.
alarm code.
3215 High voltage High voltage did not Check Polymer, Anode,
stabilization error stabilize within the and Cathode levels and for
required time the presence of bubbles.
Check Anode electrode for
damage.
alarm code.
3220 High voltage arcing Possible moisture Remove any liquid around
detected in and around the the septa, Cathode Buffer
septa, Cathode Buffer Cartridge, oven and
Cartridge, oven or the autosampler.
autosampler caused Check the Anode electrode
arcing for damage.
Contact Technical Service
if damaged or arcing is
observed.

Error Messages

3299 High voltage internal High voltage internal Restart the instrument.
processing error software error detected If alarm persists, contact
3315 Laser output power Laser power did not Restart the instrument.
stabilization error stabilize within the If alarm persists, contact
required time Technical Service with
3320 Laser output power is Laser power is too low Restart the instrument.
abnormal If alarm persists, contact
3321 Laser warning detected Laser is nearing the end Contact Technical Service
of usable life with alarm code indicated.
3399 Laser internal Laser internal software Restart the instrument.
3403 Data collection timeout Data collection time Restart the instrument.
error exceeds sampling time If alarm persists, contact
and data collection has Technical Service with
failed alarm code indicated.
3404 Data collection internal Rate of data collection Contact Technical Service
buffer overflow error exceeded the memory with alarm code indicated.
buffer capacity of the
instrument
3405 Data error Data binning pattern is Restart the instrument.
inconsistent If alarm persists, contact
3420 CCD camera CCD camera Check that the ambient
temperature error temperature is temperature is in the
abnormal allowable range of +15°C
to +30°C (+60°F to + 85°F).

Error Messages

3421 CCD camera CCD camera Restart the instrument.
temperature is too high temperature exceeds Check that the ambient
the upper limit temperature is in the
to +30°C (+60°F to + 85°F).
3422 CCD camera CCD camera Restart the instrument.
temperature sensor temperature sensor has Check that the ambient
error failed temperature is in the
allowable range of +15 to
+30°C (+60 to + 85°F).
3431 CCD camera controller CCD camera controller Restart the instrument.
error has failed Check that the ambient
to +30°C (+60°F to + 85°F).
3499 CCD camera internal CCD internal software Restart the instrument.
3520 Cartridge loading Autosampler movement Make sure nothing is
timeout error has failed blocking the movement of
the autosampler.
Check the anode electrode
and capillary for damage.
Restart the instrument.
3521 Autosampler home Autosampler home Restart the instrument.
sensor error sensor has failed If alarm persists, contact

Error Messages

3522 Autosampler Autosampler movement Make sure nothing is
movement error is out of its movable blocking the movement of
range the autosampler.
3523 Autosampler controller Autosampler controller Make sure nothing is
communication error communication has blocking the movement of
failed the autosampler.
3599 Autosampler internal Autosampler internal Restart the instrument.
processing error software error detected If alarm persists, contact
3620 Polymer delivery unit Polymer delivery unit Restart the instrument.
home sensor error home sensor has failed If alarm persists, contact
3621 Polymer delivery unit Plunger movement has Check the Polymer
plunger timeout error failed Cartidge is installed
correctly.
3622 Polymer delivery unit Polymer injection has Check the Polymer
injection timeout error failed Cartidge is installed
correctly.

Error Messages

3623 Polymer delivery unit Polymer cartridge Check the Polymer
compression timeout compression has failed Cartidge is installed
error correctly.
3624 Cartridge connection Cartridge connection Check the Polymer
timeout error has failed Cartidge is installed
correctly.
3625 Polymer leak detected Polymer is leaking - Replace the polymer
check for evidence of cartridge.
leaks If alarm persists, Contact
3626 Polymer volume is Polymer volume is too Check the Polymer
insufficient low Cartidge volume.
Replace the Polymer
Cartidge.
3627 Plunger movement Plunger movement is Check the Polymer
error out of its movable range Cartidge is installed
correctly.
3628 Polymer delivery Polymer delivery Restart the instrument.
unit controller unit controller If alarm persists, contact
communication error communication has Technical Service with
failed alarm code indicated.
3699 Polymer delivery unit Polymer delivery unit Restart the instrument.
internal processing internal software error If alarm persists, contact
error detected Technical Service with
3705 Interlock defeat switch Service maintenance Restart the instrument.
has been disabled mode has finished

Error Messages

3720 Ambient temperature Ambient temperature is Check that the ambient
is out of operational too high or low temperature is in the
range allowable range of +15°C
to +30°C (+60°F to + 85°F).
3721 Instrument ambient Instrument ambient Restart the instrument.
temperature sensor temperature sensor has If alarm persists, contact
error failed Technical Service with
3730 Data transfer error Data transfer has failed Restart the instrument.
3811 Detection heater Ambient temperature is Ensure that the over door
temperature outside too high or low is closed properly.
tolerance Check that the ambient
to +30°C (+60°F to + 85°F).
3812 Detection heater high Detection heater Restart the instrument.
temperature error temperature exceeds If alarm persists, contact
the upper limit Technical Service with
3815 Detection heater Detection heater Ensure that the door is
stabilization error temperature did not closed properly.
stabilize within the Check that the ambient
required time temperature is in the
to +30°C (+60°F to + 85°F).
3820 Detection heater Detection heater Restart the instrument.
temperature sensor temperature sensor has If alarm persists, contact
error failed Technical Service with
3899 Detection heater Detection heater internal Restart the instrument.
internal processing software error detected If alarm persists, contact
error Technical Service with

Troubleshooting 12
For questions not addressed here, contact your local Promega Branch Office or Distributor.
Contact information available at: www.promega.com
E-mail: genetic@promega.com
12.1 Instrument
Symptom Causes and Comments

No response from the touch Possible communication error. Shutdown instrument as
panel screen indicated in Section 10. Restart instrument as described in
Section 2.1. If this fails to restore the responsiveness to the
touch screen, contact Promega Technical Services.
Unstable current Inspect Spectrum Compact Polymer Cartridge for the
presence of bubbles. If bubbles are present, replace
polymer cartridge. Contact Promega Technical Services.
Anode and/or cathode ends of capillary not completely
submerged due to evaporation of buffers during a
prolonged period of non-use of the Spectrum Compact CE
System.
High run current Old polymer (on instrument for more than 2 weeks) and
polymer that is past its expiration date can have higher than
normal current during electrophoresis and longer run times,
especially for larger fragments. Replace with a Spectrum
Compact Polymer Cartridge that is within its expiration
date.
High voltage, low current Check anode electrode to see if it is loose or damaged
(bent or broken). If anode electrode is damaged contact
Promega Technical Services.
Changing baseline during Contaminants present in electrophoretic system. Replace
electrophoresis with new Spectrum Compact Capillary, Polymer, ABC and
CBC cartridges.

Troubleshooting

Poor quality data on Spectrum Damage to a capillary or capillaries may result in polymer
Compact Capillary Cartridge leakage. Check the Spectrum Compact Capillary Cartridge
with less than 200 injections for evidence of polymer leakage (white crystals appearing
somewhere along length of capillary). If damage is
detected, replace the Spectrum Compact Capillary
Cartridge.
Old polymer (on instrument for more than 2 weeks)
and/or polymer that is past its expiration date was used.
Install a fresh Spectrum Compact Polymer Cartridge and
reinject samples. Other symptoms of old polymer include
higher than normal current during electrophoresis and
longer run times, especially for larger fragments.
Anode and/or cathode ends of capillary dried out due to
evaporation of buffers during a prolonged period of non-use
of the Spectrum Compact CE System. Discard the dried out
Spectrum Compact Capillary Cartridge and replace with a
new Spectrum Compact Capillary Cartridge. If instrument
will not be used for an extended period of time (>2 weeks),
uninstall the Spectrum Compact Capillary Cartridge and
perform the long-term shutdown procedure as described in
Section 10.2.
Poor-quality formamide used with high conductivity.
Prepare sample with fresh Hi-Di™ formamide.
Spikes in data Ensure that the Spectrum Compact Polymer Cartridge is
within the expiration date. If expired, replace with a fresh
Spectrum Compact Polymer Cartridge.
Inspect the Spectrum Compact Polymer Cartridge for the
presence of bubbles. If bubbles are present, replace with
a new polymer cartridge. Contact Promega Technical
Services.
Contaminants or crystals in Spectrum Compact Polymer
Cartridge. Warm to room temperature before use. If you
observe a precipitate, gently warm the Spectrum Compact
Polymer Cartridge to dissolve the precipitate before use.
For other contaminants, replace with a new Spectrum
Compact Polymer Cartridge.

Troubleshooting
12.2 Spatial Calibration

No peaks detected in any Spectrum Compact Capillary Cartridge not installed
capillary or abnormal peak correctly. Reinstall Capillary Cartridge and perform a spatial
morphology for each capillary calibration with a polymer fill as described in Section 4.1.
resulting in failing spatial Confirm that the array window is seated on the instrument.
calibration. Spatial calibration performed on a new Spectrum Compact
Capillary Cartridge without a polymer fill. Fill the Spectrum
Compact Capillary Cartridge with polymer and perform a
spatial calibration as described in Section 4.1.
Damaged Spectrum Compact Capillary Cartridge. Inspect
Capillary Cartridge for any damage or defects. If damage is
observed, replace with an undamaged Spectrum Compact
Capillary Cartridge.
12.3 Spectral Calibration

No peaks detected in one Incorrect matrix standard used for dye set. Confirm that the
or more dye channels for correct matrix standard was run with the correct dye set.
matrix standard Bubbles in the sample well. Centrifuge 8-well strip tube to
remove air bubbles and repeat spectral calibration as per
Section 4.2.
Confirm that four wells of 8-well strip tube containing matrix
standard have been loaded into Sample Cartridge in positions
A1 through A4. If matrix standard containing wells are not in
these positions, they will not be injected and no peaks will be
detected.
Poor-quality formamide used with high conductivity. Prepare
sample with fresh Hi-Di™ formamide.
Reboot the Spectrum Compact CE System. Ensure that
the oven is preheated to 60°C prior to performing spectral
calibration.

Troubleshooting

No peaks detected in one The cathode end of the Spectrum Compact Capillary Cartridge
or more dye channels for did not enter the sample, preventing electrokinetic injection of
matrix standard (continued) the matrix standard. Check the volume of sample. Volumes of
sample as low as 9µl result in successful injection, but lower
volumes will increase the likelihood for injection failures. If
insufficient volume is present, increase the volume to >9µl and
repeat spectral calibration. If volume is sufficient and no peaks
are detected, contact Promega Technical Services.
Confirm that the matrix standard was prepared correctly.
Check the matrix standard, reagent expiration date and storage
conditions. Refer to the Matrix Standard Instructions for Use
for additional troubleshooting suggestions.
Spectral calibration fails Check the Raw Data tab of the failed capillaries. Look for signs
of low or high peak heights, incorrect dye order for matrix
standard (may indicate incompatible dye set used for matrix
standard), high baseline noise, spikes or unexpected additional
peaks that migrate before the matrix standard peaks.
Incorrect matrix standard used for dye set. Confirm that the
correct matrix standard was run with the correct dye set.
Peak present for matrix standard in raw data but too low for
generation of a spectral calibration (less than 500RFU). Check
the matrix standard, reagent expiration date and storage
Poor-quality formamide used with high conductivity. Prepare
sample with fresh Hi-Di™ formamide.
Unexpected peaks that migrate before the matrix standard
peaks may indicate carryover from a previous injection.
Replace Spectrum Compact ABC and CBC and the Spectrum
Compact Cathode Septa mat to eliminate any potential
sources of contamination from a previous injection.
Confirm that the matrix standard was prepared correctly.
Check the matrix standard, reagent expiration date and storage

Troubleshooting

Elevated spectral If elevated spectral bleedthrough is observed in one or more
bleedthrough in one capillaries after installing a new capillary cartridge, reinstall the
or more capillaries capillary cartridge. Completely remove the capillary cartridge
from the oven and reinstall as indicated in Section 3.2. Simply
lift the capillary cartridge completely out of the oven by its
yellow knob and reinstall immediately back in the oven.
Repositioning the detection unit of the capillary cartridge into
the detection window of the oven during reinstallation may
improve spectral performance.
Note: It is necessary after uninstalling and reinstalling the
capillary cartridge to perform a new spatial and spectral
calibration before running samples.

Troubleshooting
12.4 Sequencing Analysis

No peaks Poor-quality formamide used with high conductivity.
Sample loss during cleanup of sequencing sample. Repeat
the sequencing reaction.
Bubbles in the sample well. Centrifuge the 8-Well Strip Tube
to remove air bubbles, and repeat the injection.
submerged due to evaporation of buffers during a prolonged
period of non-use of the Spectrum Compact CE System.
Capillary Cartridge for any damage or defects. If damage
is observed, replace the Spectrum Compact Capillary
Cartridge.
The cathode end of the Spectrum Compact Capillary
Cartridge did not enter the sample, preventing electrokinetic
injection of the sequencing sample. Check the volume
of sample. Volumes of sample as low as 9µl result in
successful injection, but lower volumes will increase the
likelihood for injection failures. If insufficient volume is
present, increase the volume to >9µl and repeat injection of
the sequencing sample. If volume is sufficient and no peaks
are detected, contact Promega Technical Services. Ensure
the correct assay was used, because this can affect the
height of the deck tray during injection.
The sequencing reaction failed or was not sufficiently
purified. Refer to the troubleshooting section of the manual
of the sequencing kit being used.
Sequencing failed Sample loss during cleanup of sequencing sample. If the
sequencing standard control sample passed the quality
checks, repeat the sample sequencing reaction.
Incorrect run module, instrument protocol, or basecalling
protocol used. Check run modules and protocols used, and
repeat the run.
An old spectral calibration or a spectral calibration with
expired matrix standard was used. Perform a new spectral
calibration using a matrix standard within its expiration date
and re-inject the samples.

Troubleshooting

Sequencing failed (continued) Check the age of the spectral calibration being used. If old
or generated on a previous array, generate a new spectral
calibration using a new matrix standard that is within its
expiration date.
Expired reagents were used. Check that the anode and
cathode buffers have been used for <80 injections. Check
the expiration dates of all consumables. Replace expired
consumables or consumables that are beyond their usage
restrictions.
Consumables were not equilibrated to room temperature.
Ensure that consumables are allowed to come to room
temperature before a run begins. Ensure the oven was
preheated prior to the run.
Artifacts or dye blobs present. Refer to the troubleshooting
section of the manual of the sequencing kit being used.
Poor resolution due to over-injected samples. If sample
peak heights are too high either use less sample volume
and/or reduce injection time. Alternatively, reamplify with
less DNA (refer to the amplification troubleshooting section
of the manual of the sequencing kit being used).
Poor resolution due to old polymer (on instrument for more
than 2 weeks) or polymer that has passed its expiration
date. Install a fresh Spectrum Compact Polymer Cartridge,
and reinject samples. Other symptoms of old polymer
include higher than normal current during electrophoresis
and longer run times, especially for larger fragments.
A Spectrum Compact Capillary Cartridge with more than
200 injections was used. Use after this number of injections
may result in poor resolution. Replace Spectrum Compact
Capillary Cartridge, and reinject samples.
Insufficient number of bases Run time was too short. Increase the run time in the
collected when using the fast instrument protocol of the fast sequencing assay. Testing
sequencing assay at Promega has shown that adding up to 2 minutes
additional run time can result in longer reads. To edit the
instrument protocol, see Section 7.

Troubleshooting

Signal too high Sample concentration was too high. Dilute the sample and/
or repeat injection with a reduced injection time.
Too much template was added to the sequencing reaction.
Refer to the troubleshooting section of the manual of the
sequencing kit being used.
Signal too low Poor-quality formamide used with high conductivity.
Sample loss during cleanup of sequencing sample. Repeat
the sequencing reaction.
Injection time or voltage was too low. If a custom assay
was used, increase the injection time or voltage.
Poor signal and/or capillary to If low signal and/or high variation in signal from capillary
capillary signal variation to capillary is observed after installing a new capillary
cartridge, reinstall the capillary cartridge. Completely
remove the capillary cartridge from the oven and reinstall
as indicated in Section 3.2 Simply lift the capillary cartridge
completely out of the oven by its yellow knob and reinstall
immediately back in the oven. Repositioning the detection
unit of the capillary cartridge into the detection window of
the oven during reinstallation can improve overall signal
and reduce variation in signal from capillary to capillary.

Troubleshooting
12.5 Fragment Analysis

No peaks Poor-quality formamide was used with high conductivity.
Bubbles were present in the sample well. Centrifuge the
8-Well Strip Tube to remove air bubbles, and reinject the
samples.
If peaks are detected at the expected height for your
internal lane standard, this indicates that injection is
performing as expected, and the absence of sample
peaks may be due to poor amplification with the fragment
analysis kit. Refer to the amplification troubleshooting
section of the manual of the fragment analysis kit being
used.
the Capillary Cartridge for any damage or defects. If
damage is observed, replace with an undamaged Spectrum
Compact Capillary Cartridge.
The cathode end of the Spectrum Compact Capillary
Cartridge did not enter the sample, preventing electrokinetic
injection of the fragment analysis sample. Check the
volume of sample. Volumes of sample as low as 9µl result
in successful injection, but lower volumes will increase
the likelihood for injection failures. If insufficient volume is
present, increase such that the volume is above minimum
required and repeat injection of fragment analysis sample.
If volume is sufficient and no peaks are detected, contact
Promega Technical Services.
submerged due to evaporation of buffers during a
prolonged period of non-use of the Spectrum Compact CE
System.

Troubleshooting

Peak intensity too high If peaks are detected at expected height for your internal
lane standard, this indicates that injection is performing
as expected, but the high intensity peaks in your sample
may be a result of over-amplification of template DNA
with the fragment analysis kit. Refer to the amplification
troubleshooting section of the manual of the fragment
analysis kit being used.
If internal lane standard peaks are of higher signal intensity
than expected as well as those in your sample, then the
injection voltage and/or time may be too high and/or that
the volume of internal lane standard in the loading cocktail
is too high. Ensure that the correct volume of internal lane
standard and sample was added to the loading cocktail and
reduce if volumes are too high. If volumes of internal lane
standard and sample are correct, repeat injection with a
reduced injection time.
Peak intensity too low Poor-quality formamide used with high conductivity.
Salt from the amplification reaction can compete with
amplified DNA for electrokinetic injection. Adding too much
volume of amplification reaction to the sample loading
cocktail can reduce peak heights. If higher signal is desired,
either reamplify your sample with more DNA (refer to the
amplification troubleshooting of the fragment analysis kit
being used) or repeat injection with an increased injection
time.
Poor resolution Samples were over-injected. If sample peak heights are
too high, use less sample volume and/or reduce injection
time. Alternatively, reamplify with less DNA (refer to the
amplification troubleshooting section of the manual of the
fragment analysis kit being used).
Old polymer (on instrument for more than 2 weeks) and/
or polymer that has passed its expiration date was used.
Install a fresh Spectrum Compact Polymer Cartridge and
reinject samples. Other symptoms of old polymer include
higher than normal current during electrophoresis and
longer run times, especially for larger fragments.
Spectrum Compact Capillary Cartridge with more than 200
injections was used. Greater than 200 injections may result
in poor resolution. Replace Spectrum Compact Capillary
Cartridge and reinject samples.

Troubleshooting

Poor signal and/or capillary to If low signal and/or high variation in signal from capillary
capillary signal variation to capillary is observed after installing a new capillary
cartridge, reinstall the capillary cartridge. Completely
remove the capillary cartridge from the oven and reinstall
as indicated in Section 3.2. Simply lift the capillary cartridge
completely out of the oven by its yellow knob and reinstall
immediately back in the oven. Repositioning the detection
unit of the capillary cartridge into the detection window of
the oven during reinstallation can improve overall signal
and reduce variation in signal from capillary to capillary.

Protocol and Strip Setup Tools
for Spectrum Compact 13
Two Excel® macro-enabled workbooks are provided that can be used to create .xml files on a
computer that is not connected to the Spectrum Compact CE System. The following functions
can be imported via a USB drive into the Spectrum Compact Control Software as described in
Sections 5.3.4 and 7.5:
1. Assays and Protocols (Protocol Setup Tool for Spectrum Compact)

2. Strip Information (Strip Setup Tool for Spectrum Compact)
The workbook files can be downloaded at www.promega.com/SpectrumWorkbooks.
Enter your contact information, and you will be directed to download a .zip file with the two
workbooks. Save all files to an easily accessible location on your computer.
13.1 Recommended System Requirements

The following PC system requirements must be met for these tools to run:
1. Microsoft® Windows® 7/32 bit, 64bit or Windows® 10/64bit

2. Microsoft® Excel® 2016
13.2 Spreadsheet Installation

1. Copy each of the setup.exe applications to separate Strip Setup and Protocol Setup folders
on your PC. The installation process for both tools is the same. Representative instructions
for installing the Strip Setup Tool for Spectrum Compact are given below.

Protocol and Strip Setup Tools for Spectrum Compact
2. Run the setup.exe application by right clicking on the setup.exe application and “Run as
administrator” to initiate installation. A warning screen may appear, depending on the
operating system (Figure 185, example from Windows® 10 operating system). Select More
info and then Run Anyway (Figure 186).
16286TA
Figure 185. Windows® 10 Warning Window.
16287TA
Figure 186. Windows® 10 Warning Window: Run Anyway.

3. The Strip Setup Tool for Spectrum Compact InstallShield Wizard window will be displayed
(Figure 187). Select Next.
16288TA
Figure 187. InstallShield Wizard window.
4. The Ready to Install the Program window appears (Figure 188). Select Install.
16289TA
Figure 188. Ready to Install the Program window.

5. The InstallShield Wizard Completed window is displayed (Figure 189) upon successful
installation of the tool. Select Finish to exit out of the InstallShield window.
16290TA
Figure 189. Ready to Install the Program window.
6. A shortcut to each tool is placed on your PC’s desktop. Both tools are located on the PC’s
C drive in a folder called Compact CE.
Note: Upon launching these tools a security warning ribbon may appear along the top of
the screen stating that “Some active content has been disabled. Click for more details”.
Select Enable Content in this security warning ribbon to enable fully functionality of these
tools.
13.3 Protocol Setup Tool for Spectrum Compact

The Protocol Setup Tool for Spectrum Compact is accessed by opening the ‘Protocol Setup
Tool for Spectrum Compact.xlsm’ Excel® macro-enabled workbook. This tool enables user to
create and edit the following assays and protocols:
1. Assay
2. Instrument Protocol
3. Basecalling Protocol
4. Sizecalling Protocol
5. Size Standard Protocol

Assays and protocols created or edited using this tool will be outputted as .xml files. These
files can then be imported into the the Spectrum Compact Control Software as described
in Section 7.5.2. In this way, the same assays and protocols may be installed on multiple
Spectrum Compact CE Systems. In addition, assays and protocols exported from the
Spectrum Compact Control Software (Section 7.5.1) can be opened using the Protocol Setup
Tool for Spectrum Compact and user-defined protocols (but not preloaded protocols) may be
edited in the Protocol Setup Tool for Spectrum Compact.
Notes:
1. Only user-defined protocols can be exported from one instrument and imported into
another.
2. Preloaded protocols exported from the Spectrum Compact CE System Software
(Section 7.5.1) are visible after importing into the Protocol Setup Tool for Spectrum
Compact, but are greyed out and not available for editing. Instead, they may be duplicated
to make a copy that can then be edited. Preloaded protocols are not available for import
when the .xml file is subsequently imported into another Spectrum Compact Control
Software as described in Section 7.5.2.
3. Multiple assays and protocols may be created and saved in one protocol .xml file. In this
way, multiple assays and protocols can be made available on one protocol .xml file. These
multiple assays and protocols are then available for individual import on the Spectrum
Compact CE System (see Section 7.5).
13.4 Editing Existing Assays and Protocols

User-defined assays and protocols may be edited directly (i.e., without duplicating) or
duplicated to create new assays and protocols via use of the duplicate function on each assay
and protocol setup worksheet following import of a protocols .xml file into the Protocol Setup
Tool for Spectrum Compact. This duplicate function essentially serves as a Save As function,
instead of overwriting the parameters in the existing user-defined assay or protocol that is
being used as a template to create a new assay or protocol. The following table lists rules for
characters that can be used when naming new assays or protocols.
Note: Preloaded assays and protocols may be duplicated to serve as a template for the
creation of new user-defined assays or protocols, but cannot be edited directly.
1 to 40 characters
Numbers

13.4.1 Importing Protocol .xml File into Protocol Setup Tool for Spectrum Compact
1. Open the ‘Protocol Setup Tool for Spectrum Compact.xlsm’ Excel® macro-enabled
workbook. The ‘Main’ worksheet will be displayed (Figure 190).
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Figure 190. Main worksheet of the Protocol Setup Tool for Spectrum Compact.
2. Selecting Open brings up a browsing window (Figure 191) to allow you to navigate to the
location of a protocols .xml file previously exported from a Spectrum Compact CE System
(Section 7.5.1) and transferred via a USB drive to the PC.
3. Select the desired protocols .xml file and select Open on the browsing window (Figure 191).
16292TA
Figure 191. Browsing window.

4. A Microsoft® Excel® window will be displayed stating that the “Protocol file read complete”.
Select OK to close this window. The file path of the imported protocol .xml file will appear in
the Protocol File Name box of the Protocol Setup Tool for Spectrum Compact.
5. Information on individual protocols or assays can be accessed by either selecting Setup on
the ‘Main’ worksheet or selecting the tab at the bottom for the appropriate setup worksheet
(Figure 190).
13.4.2 Editing Imported Instrument Protocols

1. Open the ‘Instrument Protocol Setup’ worksheet by either selecting Setup on the
Main worksheet or selecting the tab at the bottom for the appropriate setup worksheet
(Figure 190).
2. Preloaded instrument protocols exported from the Spectrum Compact CE System Control
Software are greyed out and not available for direct editing, but may be duplicated. The
duplicated copy may be edited. User-defined instrument protocols are not greyed out
and may be directly edited, or duplicated for editing to create a new instrument protocol
(Figure 192).
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Figure 192. ‘Instrument Protocol Setup’ worksheet.
3. Select the desired instrument protocol ID, and select Duplicate at the top of the ‘Instrument
Protocol Setup’ worksheet if you are not planning to overwrite an existing user-defined
protocol (Figure 192). The new instrument protocol will have the same name as the one
that was duplicated, but with a numerical suffix (Figure 193). 16294TA
Figure 193. ‘Instrument Protocol Setup’ worksheet with Duplicated Instrument Protocol.
4. Select the cell with duplicated instrument protocol ID and rename as desired.

5. The ‘Instrument Protocol Setup’ worksheet is split into twelve columns as follows.
Note: Use scroll bar at bottom of worksheet to scroll left to right across all columns.
Minimum Maximum
Column Header Description Value Allowed Value Allowed
No. Numbering order for NA NA
instrument protocols
ID Defines the protocol name 1 Character 40 Characters
Library Type Defines whether injection NA NA
protocol is ‘Pre-Loaded’
(grayed out) or ‘User Defined’
Application Defines whether the protocol Assigned using Assigned using
is for Sequencing or drop-down drop-down
Fragment Analysis menu menu
Polymer Defines whether the protocol Assigned using Assigned using
uses Polymer4 or Polymer7 drop-down drop-down
menu menu
Run Module Preloaded modules that specify Assigned using Assigned using
run condition parameters drop-down drop-down
(injection voltage, run voltage, menu menu
oven temperature, injection
time, run time and delay time)
and on which the injection
parameters for a given
instrument protocol are based
Injection Voltage (kV) Defines the injection voltage 1 15
Injection Time (s) Defines the injection duration 1 600
Run Voltage (kV) Defines the voltage applied 1 18
during electrophoresis
Run Time (s) Defines the time needed 300 7200
to complete the run and
collect data from all labeled
fragments
Oven Temperature (°C) Defines the target oven 40 70
temperature setting for the
protocol
Data Delay Time (s) Defines the time to delay data 1 3600
collection while fragments
travel from the capillary tips
to the detection window
Note: A column header with an * symbol indicates that it is a required field. Failure to fill in
these fields will prevent the protocol from being saved.

6. Select the appropriate settings for the new instrument protocol (see also Section 7.2.1 for
information on instrument protocol settings).
7. Select the ‘Main’ worksheet tab followed by Save (Figure 190). A ‘Save As’ browse window
appears. Browse to the location (e.g., a USB drive) where you wish to save the new protocol
.xml file and save to a folder named Protocols within that location (if folder does not
already exist, create a new folder with that name).
Notes:
1. To import the Protocol .xml files onto a Spectrum Compact CE System, they must be
stored in a folder called Protocols on the USB drive. If they are stored in a different
location on the USB drive, the Spectrum Compact Control Software will not be able to
locate these files.
2. Saving can be done after each protocol is edited or after all desired protocols have
been edited.
3. If there are any invalid data errors within the new protocol.xml file being saved, an error
window will be displayed (Figure 194).
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Figure 194. Microsoft® Excel® Invalid Data Entry Error window.

13.4.3 Editing Imported Basecalling Protocol

1. Open the ‘Basecalling Protocol Setup’ worksheet by either selecting Setup on the
(Figure 190).
2. Preloaded basecalling protocols exported from the Spectrum Compact Control Software
are greyed out and not available for direct editing, but may be duplicated and the duplicate
copy edited. User-defined basecalling protocols are not greyed out and may be directly
edited, or duplicated for editing to create a new basecalling protocol (Figure 195).
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Figure 195. ‘Basecalling Protocol Setup’ worksheet.
3. Select the desired basecalling protocol ID, and select Duplicate at the top of the
‘Basecalling Protocol Setup’ worksheet if you are not planning to overwrite an existing
user-defined protocol (Figure 195). The new basecalling protocol will have the same name
as the one that was duplicated, but with a numerical suffix (Figure 196).
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Figure 196. ‘Basecalling Protocol Setup’ worksheet with duplicated Basecalling protocol.
4. Select the cell with duplicated basecalling protocol ID and rename as desired.

5. The ‘Basecalling Protocol Setup’ worksheet is split into 23 columns as follows.

Minimum Maximum
basecalling protocols
ID Defines the protocol name. 1 Character 40 Characters
Library Type Defines whether basecalling NA NA
protocol is Pre-Loaded (greyed
out) or User Defined.
Mixed Base (is Use) Defines whether the mixed Unused Use
base setting is enabled. See
Section 7.2.2 for a description
of the Mixed Base function.
Mixed Base Defines minimum height of 1% 99%
(Secondary Peak) minor secondary peak as a
percentage of the major peak
at the same position before
that peak is identified as a
mixed base.
Clear Range Defines whether the Unused Use
First bp–Last bp basecalling protocol makes
(is Use) use of the clear range (by
First bp–Last bp) setting. See
of the ‘Clear Range First bp–
Last bp’ function.
Clear Range First Defines whether the Last bp Bases to trim
bp–Last bp (Last bp basecalling protocol that is from 3´ end
Setting Method) using the clear range (by First
bp–Last bp) setting is doing so
by one of two methods:
• Last bp
• Base to trim from 3´ end
See Section 7.2.2 for a

description of the ‘Clear Range
First bp–Last bp’ function.

Minimum Maximum
Clear Range First Defines the first bp in the 1 1200
bp–Last bp [First bp sequence to be considered for
(bp)] analysis.
Note: This value should be
smaller than that chosen
for the 3´ end point (last bp
position to be considered for
analysis). See Section 7.2.2
for a description of the ‘Clear
Range First bp–Last bp’
function.
Clear Range First Defi nes the last bp in the 1 1200
bp–Last bp [Last bp sequence to be considered
(bp)] for analysis when using the
‘Last bp’ method for setting
the last bp to be considered for
analysis.
larger than that chosen for the
first bp in the sequence to be
considered for analysis. See
of the ‘Clear Range First bp–
Last bp’ function.
Clear Range First Defines the number of bases 1 1200
bp–Last bp [Bases to be removed from the 3´ end
to trim from 3´ end of the sequence when using
(bp)] the ‘Bases to trim from 3´ end’
method for setting the last bp
to be considered for analysis.
Note: This value should not
be so large as to result in
trimming of bases back before
the first bp being considered
for analysis. See Section 7.2.2
for a description of the ‘Clear
Range First bp–Last bp’
function.

Minimum Maximum
Clear Range Quality Defines whether the Unused Use
Value (is Use) basecalling protocol makes
use of the clear range (by
Quality Value) setting. See
of the the ‘Clear Range Quality
Value’ function.
Clear Range Quality Defines the minimum number 1 1200
Value [fewer than of bases that can have
(bp)] a Quality Value (QV) less
than that set in the ‘Have
QVs less than’ column. See
of the ‘Clear Range Quality
Value’ function.
Clear Range Quality Defines the sliding window of 1 1200
Value [bases out of bases that cannot have more
(bp)] than the number of bases
specified in the ‘fewer than
(bp)’ column with a Quality
Value (QV) less than that set
in the ‘Have QVs less than’
column. See Section 7.2.2 for a
Quality Value’ function.
Clear Range Quality Defines the minimum Quality 1 60
Value (Have QVs Value (QV) above which data
less than) are considered of acceptable
quality. See Section 7.2.2 for a
Quality Value’ function.
Sequencing Quality Defines whether the Unused Use
[Contiguous Read basecalling protocol makes
Length (bp)] (is Use) use of the Contiguous Read
Length (CRL) parameter
when evaluating sequencing
description of the ‘Sequencing
Quality’ function.

Minimum Maximum
Sequencing Quality Defines the minimum 1 800
[Contiguous Read CRL below which data are
Length (bp)] (< Fail) considered of unacceptable
Sequencing Quality CRL values equal to or above 1 800
[Contiguous Read this value are considered
Length (bp)] (Pass ≤) of acceptable quality. See
of the ‘Sequencing Quality’
function.
[QV20+ (bp)] (is Use) basecalling protocol makes
use of the QV20+ parameter
when evaluating sequencing
Sequencing Quality Defines the minimum 1 800
[QV20+ (bp)] (< Fail) QV20+ below which data are
considered of unacceptable
Sequencing Quality QV20+ values equal to 1 800
[QV20+ (bp)] (Pass or above this value are
≤) considered of acceptable
(Trace Score) (is basecalling protocol makes
Use) use of the Trace Score
parameter when evaluating
sequencing quality. See
of the ‘Sequencing Quality’
function.

Minimum Maximum
Sequencing Quality Defines the minimum Trace 1 60
(Trace Score) (< Fail) Score below which data are
considered of unacceptable
Sequencing Quality QV20+ values equal to 1 60
(Trace Score) or above this value are
(Pass ≤) considered of acceptable
6. Select the appropriate settings for the new basecalling protocol (see also Section 7.2.2 for
information on basecalling protocol settings).
Notes:
locate these files.
been edited.
3. If there are any invalid data errors within the new protocol.xml file being saved, an error
window will be displayed similar to that shown in Figure 194, but specific for
basecalling protocols.

13.4.4 Editing Imported Sizecalling Protocol

1. Open the ‘Sizecalling Protocol Setup’ worksheet by either selecting Setup on the
(Figure 190).
2. Preloaded sizecalling protocols exported from the Spectrum Compact Control Software
copy edited. User-defined sizecalling protocols are not greyed out and may be directly
edited, or duplicated for editing to create a new sizecalling protocol (Figure 197).
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Figure 197. ‘Sizecalling Protocol Setup’ worksheet.
3. Select the desired sizecalling protocol ID, and select Duplicate at the top of the ‘Sizecalling
Protocol Setup’ worksheet if you are not planning to overwrite an existing user-defined
protocol (Figure 197). The new sizecalling protocol will have the same name as the one
that was duplicated, but with a numerical suffix (Figure 198).
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Figure 198. ‘Sizecalling Protocol Setup’ worksheet with duplicated Sizecalling protocol
4. Select the cell with duplicated sizecalling protocol ID and rename as desired.

5. The ‘Sizecalling Protocol Setup’ worksheet is split into twelve columns as follows.
Minimum Maximum
sizecalling protocols
Library Type Defines whether sizecalling NA NA
protocol is Pre-loaded (grayed
out) or User Defined.
Size Standard Defines the size standard used Assigned using Assigned using
Protocol in the sizecalling protocol. drop-down drop-down
Options for selecting a size menu menu
standard in the pull down
menu in this cell are limited to
the size standard present on
the ‘Size Standard Protocol
Setup’ worksheet.
Analysis Range Defines the range in scan Partial Full
(Scan No.) (Full/ number/data points from
Partial) which to process the data for
peak detection. Two options
are available:
• Full
• Partial

description of the ‘Analysis
Range’ function.
Analysis Range Defines the start point for data 0 32767
(Scan No.)(Start analysis (scan number/data
Point) points) when partial analysis is
chosen. See Section 7.2.3 for
a description of the ‘Analysis
Range’ function.
Note: Numerical value for Start
Point should always be lower
than the numerical value for
Stop Point.

Minimum Maximum
Analysis Range Defines the stop point for data 0 32767
(Scan No.) (Stop analysis (scan number/data
Point) points) when partial analysis is
chosen. See Section 7.2.3 for
a description of the ‘Analysis
Range’ function.
Note: Numerical value for Stop
Point should always be higher
than the numerical value for
Start Point.
Size Standard Peak Defines the minimum RFU 1 30000
Amplitude Threshold value at which to size and call
(RFU) a peak in the size standard
dye channel. Peaks in the
size standard must exceed
the peak amplitude threshold
value in order for that peak
to be considered in the sizing
algorithm. See Section 7.2.3
for a description of the ‘Peak
Amplitude Threshold’ function.
Size Quality(< Fail) Defines the minimum Size 0.001 1
Quality (SQ) value below
which data are considered of
unacceptable sizing quality.
description of the ‘Size Quality’
function.
smaller than that entered for
Pass ≤.
Size Quality(Pass ≤) SQ values equal to or above 0.001 1
this value are considered
of acceptable quality. See
of the ‘Size Quality’ function.
larger than that entered for
< Fail.

Minimum Maximum
Electrophoresis Defines the minimum 1 1000
Quality(< Fail) Electrophoresis Quality (EQ)
value (in bp) below which
data are considered of
unacceptable electrophoresis
quality. See Section 7.2.3
for a description of the
‘Electrophoresis Quality’
function.
smaller than that entered for
Pass ≤.
Electrophoresis EQ values equal to or above 1 1000
Quality(Pass ≤) this value are considered
of acceptable quality. See
of the ‘Electrophoresis Quality’
function.
larger than that entered for
< Fail.
6. Select the appropriate settings for the new sizecalling protocol (see also Section 7.2.3 for
information on sizecalling protocol settings).
Notes:
a. To import the Protocol .xml files onto a Spectrum Compact CE System, they must be
locate these files.
b. Saving can be done after each protocol is edited or after all desired protocols have
been edited.
c. If there are any invalid data errors within the new protocol.xml file being saved, an error
window will be displayed similar to that shown in Figure 194, but specific for
sizecalling protocols.

13.4.5 Editing Imported Size Standard Protocol

1. Open the ‘Size Standard Protocol Setup’ worksheet by either selecting Setup on the
‘Main’ worksheet or selecting the tab at the bottom for the appropriate setup worksheet
(Figure 190).
2. Preloaded size standard protocols exported from the Spectrum Compact Control Software
copy edited. User-defined size standard protocols are not greyed out and may be directly
edited, or duplicated for editing to create a new size standard protocol (Figure 199).
16300TA
Figure 199. ‘Size Standard Protocol’ Setup worksheet.
3. Select the desired size standard protocol ID, and select Duplicate at the top of the ‘Size
Standard Protocol Setup’ worksheet if you are not planning to overwrite an existing user-
defined protocol (Figure 199). The new size standard protocol will have the same name as
the one that was duplicated, but with a numerical suffix (Figure 200).
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Figure 200. ‘Size Standard Protocol’ Setup worksheet with duplicated Size Standard Protocol.
4. Select the cell with duplicated size standard protocol ID and rename as desired.

5. The ‘Size Standard Protocol Setup’ worksheet is split into six columns as follows.
Minimum Maximum
No. Numbering order for size standard NA NA
protocols
Library Type Defines whether the size standard NA NA
protocol is Pre-loaded (grayed out)
or User Defined.
Size Standard Defines the pre-loaded size Assigned using Assigned using
standard upon which the new drop-down drop-down
size standard protocol is based. menu menu
Options for selecting a size
standard in the pull-down menu
in this cell are limited to the
pre-loaded size standard protocols
present on the Spectrum Compact
CE System.
Note: A new size standard
protocol cannot be created without
being based on the pre-loaded size
standards.
Dye Color Specifies the dye channel NA NA
containing the size standard
fragments (not editable).
Size Standard Defines the fragment sizes to be NA NA
Definition used for creating a sizing curve.
Orange or red shading indicates
the size is to be used. Gray
shading indicates the size will not
be used. Individual fragment sizes
can be selected or deselected by
selecting the corresponding cell on
the screen.
Note: New fragment sizes cannot
be created.

6. Select the appropriate settings for the new size standard protocol (see also Section 7.3.1
for information on size standard protocol settings).
Notes:
a. To import the Protocol .xml files onto a Spectrum Compact CE System, they must be
locate these files.
b. Saving can be done after each protocol is edited or after all desired protocols have
been edited.
c. If there are any invalid data errors within the new protocol.xml file being saved, an error
window will be displayed similar to that shown in Figure 194, but specific for size
standard protocols.
13.4.6 Editing Imported Assays

1. Open the ‘Assay Setup’ worksheet by either selecting Setup on the ‘Main’ worksheet or
selecting the tab at the bottom for the appropriate setup worksheet (Figure 190).
2. Preloaded assays exported from the Spectrum Compact Control Software are greyed out
and not available for direct editing, but may be duplicated and the duplicate copy edited.
User-defined assays are not greyed out and may be directly edited, or duplicated for editing
to create a new assay (Figure 201).
16302TA
Figure 201. ‘Assay Setup’ worksheet.

3. Select the desired assay ID, and select Duplicate at the top of the ‘Assay Setup’ worksheet
if you are not planning to overwrite an existing user-defined protocol (Figure 201). The new
assay will have the same name as the one that was duplicated, but with a numerical suffix
(Figure 202).
16303TA
Figure 202. ‘Assay Setup’ worksheet with duplicated assay.
4. Select the cell with duplicated assay ID and rename as desired.

5. The ‘Assay Setup’ worksheet is split into nine columns as follows.
Minimum Maximum
No. Numbering order for assays. NA NA
ID Defines the assay name. 1 Character 40 Characters
Library Type Defines whether the size standard NA NA
protocol is Pre-loaded (grayed out)
or User Defined.
Application Defines whether the assay is for Assigned using Assigned using
Sequencing or Fragment analysis. drop-down drop-down
menu menu
Polymer Defines whether the protocol uses Assigned using Assigned using
Polymer4 or Polymer7. drop-down drop-down
menu menu
Dye Set Drop-down box to select the Assigned using Assigned using
appropriate dye set for the drop-down drop-down
chemistry being run. menu menu
Instrument Drop-down menu to specify the Assigned using Assigned using
Protocol instrument protocol to be applied drop-down drop-down
during data collection. menu menu

Minimum Maximum
Basecalling Drop-down menu to specify the Assigned using Assigned using
Protocol basecalling protocol to be applied drop-down drop-down
Note: The ‘Basecalling Protocol’
drop-down menu is only available
for sequencing applications. The
cell is grayed out if “Fragment” is
chosen as the application type.
Sizecalling Protocol Drop-down menu to specify the Assigned using Assigned using
sizecalling protocol to be applied drop-down drop-down
Note: The ‘Sizecalling Protocol’
drop-down menu is only available
for fragment applications. The cell
is grayed out if “Sequencing” is
chosen as the application type.
these fields will prevent the assay from being saved.
6. Select the appropriate settings for the new assay (see also Section 7.2.5 for information on
assay settings).
7. It is also possible to edit specific settings within the instrument, basecalling or sizecalling
protocols selected for an assay. Select Right Double Arrow in the column header for
the desired instrument, basecalling or sizecalling protocol to be edited within the assay
(Figure 203).
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Figure 203. ‘Assay Setup’ worksheet with Double Arrow button.

8. This opens columns to the right containing the individual parameters that may be edited
for that instrument, basecalling, or sizecalling protocol as described in Sections 13.4.2–
13.4.4 (Figure 204).
Note: Right Double Arrow becomes Left Double Arrow after it is selected. Selecting Left
Double Arrow closes the detailed parameters columns for the instrument, basecalling, and
sizecalling protocols.
16305TA
Figure 204. ‘Assay Setup’ worksheet with Instrument Protocol parameters displayed.
9. Selecting Right Double Arrow in the Sizecalling Protocol column header also enables Right
Double Arrow in the Size Standard Protocol column header (Figure 205).
16306TA
Figure 205. ‘Assay Setup’ worksheet with Double Arrow button for Size Standard Protocol.

10. Select Right Double Arrow in the Size Standard Protocol column header to display the
individual size standard parameters (Figure 206) that may be edited as described in
Section 13.4.5.
Note: Edits made to the Instrument or Analysis (Basecalling or Sizecalling) Protocol within
the ‘Assay Setup’ worksheet do not change the parameters of the parent instrument and
analysis protocols originally associated with the new assay. Changes are only stored with
respect to the new assay.
16307TA
Figure 206. Size Standard Protocol parameters displayed.
Notes:
locate these files.
been edited.
3. If there are any invalid data errors within the new protocol.xml file being saved (e.g.,
assay being saved with an invalid sizecalling protocol ID that does not exist in the
‘Sizecalling Protocol Setup’ worksheet), an error window will be displayed (Figure 194).

13.5 Creating New Assays and Protocols

User-defined assays and protocols may be created directly (i.e., without duplicating) with or
without prior import of a protocols .xml file. The process for creating assays and protocols is
essentially the same as that described for editing these methods in Sections 13.4.2–13.4.6.
The main consideration when creating assays and protocols, especially without prior import of
a protocol .xml file, is that certain fields in specific columns for different assay/protocol setup
worksheets are predicated on completing prior protocols and/or selecting amplification and
polymer type as described in the following table.
Worksheet Column Pull-Down Menu Display Pull-Down Menu

Requirement Content Options
Assay Setup Dye Set • Application Type selected Available Dye Set
(fragment or sequencing) list corresponding to
the Application Type
selected.
Instrument • Application Type selected Any Protocol ID
Protocol (fragment or sequencing) on the ‘Instrument
Protocol Setup’
• Polymer Type selected worksheet with the
(Polymer4 or Polymer7) same Application
• Instrument Protocol must Type and Polymer
have been created for the Type as that selected
sample Application Type and for the assay.
Polymer Type selected for
the assay

Worksheet Column Pull-Down Menu Display Pull-Down Menu

Requirement Content Options
Assay Setup Run Module* • Application Type selected Run Module
(continued) (fragment or sequencing) corresponding to the
Instrument Protocol
• Polymer Type selected selected for the
(Polymer4 or Polymer7) assay.
• Instrument Protocol
(containing the Run Module)
must have been created for
the sample Application Type
and Polymer Type selected
for the assay
Basecalling • “Sequencing” selected as Any Protocol ID on
Protocol Application Type the ‘Basecalling
Protocol Setup’
• Basecalling Protocol must worksheet.
have been created
Sizecalling Protocol • “Fragment” selected as Any Protocol ID
Application Type on the ‘Sizecalling
Protocol Setup’
• Sizecalling Protocol must worksheet.
have been created
Size Standard • “Fragment” selected as Any Protocol ID on
Protocol Application Type the ‘Size Standard
Protocol Setup’
• Sizecalling Protocol must worksheet.
have been created
Instrument Run Module* • Application Type selected Run Module
Protocol (fragment or sequencing) corresponding to
Setup the Application Type
• Polymer Type selected and the Polymer
(Polymer4 or Polymer7) Type selected for the
instrument protocol.
Sizecalling Size Standard • Size Standard Protocol must Any Protocol ID on
Protocol Protocol* have been created the ‘Size Standard
Setup Protocol Setup’
worksheet.
*These columns are only available after selecting Right Double Arrow (see Section 13.4.6).

13.6 Deleting Assays and Protocols

User-defined assays and protocols may be deleted one protocol at a time within each
worksheet.
1. Select cell containing the Protocol ID that you wish to delete.

2. Select Delete at the top of the protocol setup worksheet.
3. A warning window will appear asking ‘Are you sure you want to delete the Protocol?’
4. Select Yes to delete the protocol.
5. Select No to cancel out of the deletion step.
13.7 Strip Setup Tool for Spectrum Compact

The ‘Strip Setup Tool for Spectrum Compact’ is accessed by opening the ‘Strip Setup Tool for
Spectrum Compact.xlsm’ Excel® macro-enabled workbook. This tool enables the user to create
and edit information for up to four strips (i.e., maximum number of strip for one run) in one .xml
file that can then be imported into the Spectrum Compact Control Software as described in
Section 5.3.4. The following table lists rules for characters that can be used for a Strip ID and
Sample Name:
1 to 30 characters
Numbers
Notes:
1. While only 30 characters may be used for a strip ID, up to 50 characters are allowed for
individual sample names.
2. Multiple strips may be created and saved in one strip .xml file. In this way, multiple strips
can be made available on one strip .xml file. These strips are then available for individual
import when setting up a run on the Spectrum Compact CE System (see Section 5.3.4).

13.7.1 Opening Protocol .xml File within Strip Setup Tool for Spectrum Compact
To use the Strip Setup Tool for Spectrum Compact to create or edit a strip information .xml
file, a protocol .xml file (created using the Protocol Setup Tool for Spectrum Compact and
containing protocols and assays to be used in setting up the strip) must be opened within the
Strip Setup Tool for Spectrum Compact.
1. Select Open on the right-hand side of the Protocol File Name box (Figure 207). This opens
a browsing window. Browse to the location of the protocols .xml file created using the
Protocols Setup Tool for Spectrum Compact and select Open (Figure 208). A Microsoft®
Excel® window will appear stating “Protocol file read complete”.
2. Select OK to close out of this window. The protocol .xml file name is displayed at the top of
the Strip Setup Tool for Spectrum Compact (Figure 209).
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Figure 207. Strip Setup Tool for Spectrum Compact. 16309TA

16310TA
Figure 209. Strip Setup Tool for Spectrum Compact with Protocol File Name selected

1. Select the cell immediately to the right of the Strip Information ID cell and enter the new
Strip Information ID (Figure 210).
2. Select the cell immediately to the right of the Application Type cell and use the pull-down
menu to select the application type:
• Sequencing-Polymer7
• Fragment-Polymer4
• Fragment-Polymer7
3. For each lane (i.e., strip), select a Sample Type for each well that will contain a sample by
selecting that cell (Figure 210).
• Select S for Sample
• Select C+ for Positive Control
• Select C- for Negative Control
• Select A for Allelic Ladder
Notes:
a. Sample type options vary depending on whether fragment or sequencing are chosen
for application type. See Sections 5.3.1 and 5.4.1 for description of sample types
available for fragment and sequencing analysis, respectively.
b. A sample type other than “Unused” must be assigned to at least one well in each
injection set (wells 1–4 or wells 5–8). If all four wells in an injection set are assigned as
“Unused”, the injection set will not be run. If all eight wells in a strip are assigned as
“Unused”, a warning message will be displayed when trying to run on the Spectrum
Compact CE System.

16311TA
Figure 210. Strip Setup Tool for Spectrum Compact with Sample Type selected.
Enter a sample name for each well position by selecting the Sample Name cell adjacent to the
well number and entering the sample name (Figure 211).
16312TA
Figure 211. Strip Setup Tool for Spectrum Compact with Sample Names entered.

4. To assign an assay to an injection set (set of four wells), select the cell under the Assay
column to the right of the cell labelled 1st. This will activate a pull-down menu (Figure 212).
Select the desired assay from the available list. Repeat for all injection sets.
Note: When entering sample names in the Strip Setup Tool for Spectrum Compact, copy
and paste can be used as well as fill-down commands.
16313TA
Figure 212. Strip Setup Tool for Spectrum Compact with Assay pull-down menu.
5. Repeat these steps for the 2nd assay field if a second assay will be run for the strip.
Note: The assays available in the 2nd assay field are filtered based on the dye set in the
assay selected in the 1st assay field. For example, if a ‘Promega_6-dye’ dye set based
assay is chosen in the 1st assay field, then only assays using that same dye set are
available as an option in the 2nd assay field. In this way, injections can be duplicated with
the same assay conditions by choosing the same assay in the 2nd assay field as that used
in the 1st assay field. Duplicate injections of the same assay conditions can be run by
using the Duplicate function of the ‘Edit Injection List’ screen (see Section 5.6).

6. Select Apply to move the newly created strip information to the Strip Information ID List.
The name of the newly created strip will appear in this list (Figure 213).
Notes:
1. An asterisk appears in front of the newly created strip file name in the Strip Information
ID List prior to saving the strip information as a .xml file. After saving as a .xml file, the
asterisk disappears (Figure 212).
2. Multiple strips may be created and added to the Strip Information ID List prior to
saving the strip .xml file. In this way, multiple strips can be made available on one strip
.xml file. These multiple strips are then available for individual import when setting up a
run on the Spectrum Compact CE System (see Section 5.3.4).
3. Strip information may be filtered by application type (sequencing and fragment,
sequencing alone, or fragment alone) by checking boxes adjacent to “Sequencing” and
“Fragment” above the Strip Information ID List.
16314TA
Figure 213. ‘Strip Setup Tool for Spectrum Compact’ with new strip in Strip Information ID List.
7. By selecting either Duplicate or Delete with the new strip highlighted in Strip Information ID
List, the newly created strip can be duplicated or deleted prior to saving the strip .xml file.
8. To save the new strip information as a .xml file that can be imported into the Spectrum
Compact Control Software via a USB drive, select Save to the right of the Strip Information
File Name. A ‘Save As’ window will appear. Browse to the location (e.g., a USB drive) where
you wish to save the new strip .xml file and save to a folder named Strips within that
location (if folder does not already exist, create a new folder with that name).
Note: To import the Strips .xml files onto a Spectrum Compact CE System, they must be
stored in a folder called Strips on the USB drive. If they are stored in a different location on
the USB drive, the Spectrum Compact CE System Software will not be able to locate these
files.

9. The name and location of the new strip will now appear in the Strip Information File Name
cell (Figure 214).
16315TA
Figure 214. Strip Setup Tool for Spectrum Compact with new strip in Strip Information File Name.
13.7.3 Loading and Editing Existing Strip Information

The Strip Setup Tool for Spectrum Compact can be used to import strip .xml files and edit
these files to create new strip .xml files. To use the Strip Setup Tool for Spectrum Compact to
edit a strip .xml file, a protocol .xml file (created using the Protocol Setup Tool for Spectrum
Compact and containing protocols and assays to be used in setting up the strip) must
also be opened within the Strip Setup Tool for Spectrum Compact as described above (see
Section 13.7.1).
1. After opening a protocol .xml file within the Strip Setup Tool for Spectrum Compact, select
Open on the right-hand side of the Strip Information File Name box (Figure 215). This opens
a browsing window. Browse to the location of the strips .xml file created and select Open
(Figure 216). A Microsoft® Excel® window will appear stating “Strip information file read
complete”. Select OK to close out of this window. The strip .xml file name is now displayed at
the top of the Strip Setup Tool in the Strip Information File Name box (Figure 217).
Note: If a strip .xml file is chosen when opening a Protocol File Name or if a protocol .xml
file is chosen when opening a Strip Information File Name, a Microsoft® Excel® window will
appear stating “Cannot read protocol file. Unsupported file format.” or “Cannot read strip
information file. Unsupported file format.”, respectively. Select OK and confirm that the
correct .xml file is being opened.

16316TA
Figure 215. Strip Setup Tool for Spectrum Compact with Protocol .xml file in Protocol File Name.
16317TA

16585TA
Figure 217. Strip Setup Tool for Spectrum Compact with strip .xml file in Strip Information File Name.
2. Select the desired Strip in the Strip Information ID List on the right-hand side of the screen
followed by Load (Figure 217).
Note: Strip information may be filtered by application type (sequencing and fragment,
sequencing alone, or fragment alone) by checking boxes adjacent to “Sequencing” and
“Fragment” above the Strip Information ID List.
3. The information for that strip now appears on the left-hand side of the screen (Figure 218).
16586TA
Figure 218. Strip Setup Tool for Spectrum Compact with Strip Information ready for editing.

4. Edit the information for the new strip following the instructions for Creating New Strip
Information (Section 13.7.2). If desired, a new Strip Information ID can be assigned
(Figure 219).
16587TA
Figure 219. Strip Setup Tool for Spectrum Compact with edited new Strip Information ID.

5. Select Apply to move the newly created strip information to the ‘Strip Information ID List’.
The name of the newly created strip will appear in this list (Figure 220).
Notes:
a. An asterisk appears in front of the newly created strip file name in the Strip Information
ID List prior to saving the strip information as a .xml file. After saving as a .xml file, the
asterisk disappears (Figure 221).
b. Multiple strips may be created and added to the Strip Information ID List prior to
saving the strip .xml file. In this way, multiple strips can be made available on one strip
.xml file. These multiple strips are then available for individual import when setting up a
run on the Spectrum Compact CE System (see Section 5.3.4).
16588TA
Figure 220. Strip Setup Tool for Spectrum Compact with new strip in Strip Information ID List.
6. By selecting either Duplicate or Delete with the new strip highlighted in Strip Information ID
List, the newly created strip can be duplicated or deleted prior to saving the strip .xml file.
7. To save the new strip information as a .xml file that can be imported into the Spectrum
Compact CE System Software via a USB drive, select Save to the right of the Strip
Information File Name. A ‘Save As’ window will appear. Browse to the location (e.g., a USB
drive) where you wish to save the new strip .xml file and save to a folder named Strips
within that location (if folder does not already exist, create a new folder with that name).
The existing strip file information name may be overwritten (if saving to the same location
where the original unedited file was stored) or saved as a new name, as desired.
Note: To import the Strips .xml files onto a Spectrum Compact CE System, they must be
stored in a folder called Strips on the USB drive. If they are stored in a different location on
the USB drive, the Spectrum Compact CE System Software will not be able to locate these
files.

8. The name and location of the new strip will now appear in the Strip Information File Name
cell (Figure 221).
16589TA
Figure 221. Strip Setup Tool for Spectrum Compact with new strip in Strip Information File Name.

Reviewing System Tests 14
System Tests are performed by service engineers at time of installation of the Spectrum
Compact CE System or following a service. While these System Tests are only performed by
service engineers, the results of these System Tests may be viewed at any time by a user.
There are two types of System Test:
• Fragment System Test

• Sequencing System Test
Select System Tests on the ‘Main Menu’ screen (Figure 9) to access the ‘System Test’ screen
(Figure 222). Three options are displayed:
1. Sequencing System Test

2. Fragment System Test
3. Review Result
16498TA
Figure 222. ‘System Test’ screen.

Reviewing System Tests
Sequencing System Test and Fragment System Test are for use by the service engineer only
and their functionality is not covered in the operating manual.
Select Review Results on the ‘System Test’ screen (Figure 222) to display the ‘Result List’
16499TA
Figure 223. ‘Result List’ screen.
The list of system tests displayed can be filtered based on application type (all applications,
fragment, or sequencing) by repeatedly selecting the filter button in the top left corner of the
screen.
14.1 Reviewing Fragment System Test Results

The ‘Result List’ screen is divided into four main sections: No (the system test number),
Performed Date, Application and Details (Figure 223).
1. Use the scroll buttons to the right side of the Application column in the ‘Result List’ screen
to locate the completed system test you wish to review.
2. Select the system test you wish to review. This will display the Details section of the ‘Result
List’ screen for the selected system test (Figure 224).
3. Select View in the footer to review the detailed results of the system test in the ‘Result
View’ screen (Figure 225). View and Export do not become active until a sample is
selected.

Details
Result List
16500TA
Figure 224. ‘Result List’ screen with Selected Fragment System Test. Delete, Export, and View do not become
active until a system test is selected in the ‘Result List’ screen.
The footer provides three options.
Command Function
Delete Deletes the selected system test.
Note: A window appears after selecting Delete asking “Are you
sure you want to delete selected data?” Selecting Yes completes
the deletion process. Selecting No takes you back to the ‘Result
List’ screen.
Export Exports the selected system test report as a pdf file.
Note: A USB drive must be connected to the Spectrum Compact
CE System for the export option to function.
View Opens the Result View screen for the selected system test
4. Select View in the footer to view the list of four samples in that system test in the ‘Result
View’ screen (Figure 225).
16501TA
Figure 225. Fragment System Test ‘Result View’ screen.

5. Six columns of data are displayed with information on fragment system test performance.

No Capillary number
Sizing Precision Maximum standard deviation of allele sizing
observed across all alleles in the four Allelic
Ladder samples. To pass, this value must be
<0.16 bases.
Sizing Accuracy Maximum deviation in size (bases) of any given
allele in the Allelic Ladder, on any of the four
capillaries, relative to mean expected value for
that allele. To pass, this value must be <0.5
bases.
Fragment Electrophoresis Quality Electrophoresis Quality is the size (bases) at

which the peak width at half maximal height is
equal to the distance between two bases, as
calculated from the size standard. To pass, this
value must be ≥400 bases.
All Allele Call Indicates whether or not all the expected alleles
in the Allelic Ladder were present. Overall
evaluation (Pass/Fail).
Status All of the above parameters must pass in order
for Status to pass. Failure of any one of the
above parameters is sufficient for Status to fail.
Overall evaluation (Pass/Fail).
6. Select the line in the Result List corresponding to the system test sample you wish to
review. This will activate Export and View in the footer (Figure 226).
16502TA
Figure 226. Fragment System Test ‘Result View’ screen with selected sample.

7. Selecting Export will export the system test report as a pdf file in the same way as
selecting Export from the ‘Result List’ screen (Figure 224).
8. Select View in the footer to view the data for that sample in the ‘Graph’ screen (Figure 227).
See ‘Results’ Tab in Section 5.7, Monitoring a Run, for definitions of the navigation icons on
this screen and how to use them.
16503TA
Figure 227. Fragment System Test ‘Graph’ screen of selected sample.
14.2 Reviewing Sequencing System Test Results

The ‘Result List’ screen is divided into four main sections: No (the system test number),
Performed Date, Application and Details (Figure 223).
1. Use the scroll buttons to the right side of the Application column in the ‘Result List’ screen
to locate the completed system test you wish to review.
2. Select the system test you wish to review. This will display the Details section of the ‘Result
List’ screen for the selected system test (Figure 228).
3. Select View in the footer to view a list of samples in that run in the ‘Result View’ screen
(Figure 229). View and Export do not become active until a sample is selected.

Details
Result List
16504TA
Figure 228. ‘Result List’ screen with Selected Sequencing System Test. Delete, Export, and View do not become
active until a system test is selected in the ‘Result List’ screen.
The footer provides three options.
Command Function
Delete Deletes the selected system test.
Note: A window appears after selecting Delete asking “Are you
sure you want to delete selected data?” Selecting Yes completes
the deletion process. Selecting No takes you back to the ‘Result
List’ screen.
Export Exports the selected system test report as a pdf file.
Note: A USB drive must be connected to the Spectrum Compact
CE System for the export option to function.
View Opens the ‘Result View’ screen for the selected system test.
4. Select View in the footer to view the list of four samples in that system test in the ‘Result
View’ screen (Figure 229).
16505TA
Figure 229. Sequencing System Test ‘Result View’ screen.

5. Two columns of data are displayed with information on sequencing system test
performance.

Sequencing No Capillary number
Contiguous Read Number of contiguous bases in the sequence
Length that have an average quality value (QV) score
≥20 over a 21 base sliding window. To pass,
this value must be ≥600 bases.
6. Select the line in the Result List corresponding to the system test sample you wish to
review. This will activate Export and View in the footer (Figure 230).
16506TA
Figure 230. Sequencing System Test ‘Result View’ screen with selected sample.
7. Selecting Export will export the system test report as a pdf file in the same way as
selecting Export from the ‘Result List’ screen (Figure 228).
8. Select View in the footer to view the data for that sample in the ‘Graph’ screen (Figure 231).
See ‘Results’ Tab in Section 5.7, Monitoring a Run, for definitions of the navigation icons on
this screen and how to use them.
16507TA
Figure 231. Sequencing System Test ‘Graph’ screen of selected sample.

Summary of Changes 15
The following change was made to the 3/23 revision of this document:
1. Updated Section 10.1.

© 2020–2023 Promega Corporation. All Rights Reserved.
PowerPlex is a registered trademark of Promega Corporation.
Excel, Microsoft and Windows are registered trademarks of Microsoft Corporation. LIZ and VIC are registered trademarks
and FAM, GeneMapper, HEX, Hi-Di, NED, PET, ROX and TAMRA are trademarks of Thermo Fisher Scientific. GeneMarker is a
registered trademark of SoftGenetics.
Products may be covered by pending or issued patents or may have certain limitations. Please visit our Web site for more
information.
All prices and specifications are subject to change without prior notice.
Product claims are subject to change. Please contact Promega Technical Services or access the Promega online catalog for the
most up-to-date information on Promega products.
Not for Medical Diagnostic Use. Class 1 Laser Product.

PROMEGA CORPORATION • 2800 WOODS HOLLOW ROAD • MADISON, WI 53711-5399 USA • TELEPHONE 608-274-4330
www.promega.com • © 2023 PROMEGA CORPORATION • ALL RIGHTS RESERVED • PRICES AND SPECIFICATIONS SUBJECT TO CHANGE WITHOUT PRIOR NOTICE • TMD058 • Revised 3/23

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Spectrum Compact CE System

TMD058 | Revised 3/23

2 Spectrum Compact CE System | TMD058 | Revised 3/23

3 Spectrum Compact CE System | TMD058 | Revised 3/23

7 Managing Assays, Protocols and Dye Sets......................................... 108

8 Managing Instrument Settings.............................................................. 141

9 Instrument Information........................................................................... 158

10 Shutting Down the Instrument............................................................... 161

4 Spectrum Compact CE System | TMD058 | Revised 3/23

14 Reviewing System Tests......................................................................... 225

15 Summary of Changes.............................................................................. 232

All technical literature is available at: www.promega.com/protocols/

5 Spectrum Compact CE System | TMD058 | Revised 3/23

The Spectrum Compact CE System is intended for:

6 Spectrum Compact CE System | TMD058 | Revised 3/23

Touch Screen Panel

Front Door Door Handle

7 Spectrum Compact CE System | TMD058 | Revised 3/23

Air Intake Panel

USB Keyboard USB Bar Code

Detection Oven Door

8 Spectrum Compact CE System | TMD058 | Revised 3/23

1.2 Common Safety Precautions

9 Spectrum Compact CE System | TMD058 | Revised 3/23

1.3 Safety Symbols and Marking

Safety Symbols and Markings

Danger. Hazardous voltage. Risk of electric shock.

Warning. Sharp objects inside.

This label indicates laser radiation is present.

Symbols Explanation Symbols Explanation

Serial Number Manufacturer

Date of Manufacture Consult your local Promega

10 Spectrum Compact CE System | TMD058 | Revised 3/23

1.4 Location of Instrument Safety Symbols on Oven Door

11 Spectrum Compact CE System | TMD058 | Revised 3/23

1.5 Spectrum Compact CE System Specifications

Processing Time 30–60 minutes, depending on application

이 기기는 업무용 환경에서 사용할 목적으로 적합성평가를 받은 기기로서 가정용 환경에서

Important! Power connectors

Danger! Hazardous voltage. Risk of electric shock.

12 Spectrum Compact CE System | TMD058 | Revised 3/23

Warning! Sharp objects inside.

Warning! Sharp objects inside.

Warning! Physical injury hazard

1.6 General Warnings

13 Spectrum Compact CE System | TMD058 | Revised 3/23

Handling the instrument and peripheral devices

1.7 Product Components

Spectrum Compact CE System CE1304

• Spectrum Compact CE System

14 Spectrum Compact CE System | TMD058 | Revised 3/23

1.8 Reagents and Consumables

15 Spectrum Compact CE System | TMD058 | Revised 3/23

Important! Only use parts and devices specified by Promega Corporation

16 Spectrum Compact CE System | TMD058 | Revised 3/23

1.9 Laser Safety

The laser specifications are:

• Do not remove the instrument protective panels or safety labels.