Qubit 4 Fluorometer: Catalog Number Q33226

Qubit™ 4 Fluorometer
Catalog Number Q33226
Publication Number MAN0017209

Revision C.0
For Research Use Only. Not for use in diagnostic procedures.

Manufacturer: Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
Information in this document is subject to change without notice.

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR
SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM
THIS DOCUMENT, INCLUDING YOUR USE OF IT.
Revision history: MAN0017209
Revision Date Description

Add note about the requirement for driver installation in “Export data directly to
C.0 09 April 2018
computer”.
B.0 30 January 2018 Update Safety and EMC standards and Results screen images for quality assays.
A.0 05 October 2017 New user guide.
Important Licensing Information: This product may be covered by one or more Limited Use Label Licenses. By use of this product,
you accept the terms and conditions of all applicable Limited Use Label Licenses.
Trademarks: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Kimwipes is
a registered trademark of Kimberly-Clark Corporation. Windows is a registered trademark of Microsoft Corporation.
© 2018 Thermo Fisher Scientific Inc. All rights reserved.
ii Qubit™ 4 Fluorometer User Guide

Contents
About this guide ............................................................................................................ 3
1. Product information ................................................................................................ 5
Product contents .............................................................................................................................................. 5
Product description ......................................................................................................................................... 6
Instrument exterior components ................................................................................................................... 7
Product specifications ..................................................................................................................................... 8
2. Getting started ........................................................................................................ 9
Set up the Qubit™ 4 Fluorometer ................................................................................................................... 9
Optional: Configure instrument settings ..................................................................................................... 11
Guidelines for using the Qubit™ 4 Fluorometer ........................................................................................ 16
3. Perform assays ..................................................................................................... 17
Overview ........................................................................................................................................................ 17
Optional: Use Reagent Calculator to prepare Qubit™ Working Solution ............................................... 18
Calibrate assays on the Qubit™ 4 Fluorometer .......................................................................................... 20
Read samples ................................................................................................................................................. 24
Results ............................................................................................................................................................. 26
Fluorometer mode ......................................................................................................................................... 29
Ion Sphere™ Assay ......................................................................................................................................... 31
4. Manage data .......................................................................................................... 32
Introduction ................................................................................................................................................... 32
View detailed sample data ........................................................................................................................... 32
Rename data files........................................................................................................................................... 35
Export data ..................................................................................................................................................... 36
Delete data ...................................................................................................................................................... 39
5. Manage, import, and create assays ....................................................................... 40
Overview ........................................................................................................................................................ 40
Manage assays ............................................................................................................................................... 40
Show/Hide assays ........................................................................................................................................ 41
Move assays ................................................................................................................................................... 43
Import assays ................................................................................................................................................. 45
Create your own assay for the Qubit™ 4 Fluorometer .............................................................................. 50
6. Instrument maintenance ....................................................................................... 51
Maintenance and cleaning............................................................................................................................ 51
Software updates ........................................................................................................................................... 52
Device verification test ................................................................................................................................. 54
Qubit™ 4 Fluorometer User Guide 1

Appendix A: Troubleshooting...................................................................................... 55
Troubleshooting............................................................................................................................................. 55
Critical Qubit™ Assay considerations ......................................................................................................... 57
Appendix B: Ordering information .............................................................................. 59
Qubit™ 4 Fluorometer and accessories ....................................................................................................... 59
Appendix C: Safety ...................................................................................................... 60
Symbols on instruments ............................................................................................................................... 60
Safety labels on instruments ........................................................................................................................ 61
General instrument safety ............................................................................................................................ 62
Chemical safety .............................................................................................................................................. 63
Chemical waste safety................................................................................................................................... 64
Electrical safety .............................................................................................................................................. 65
Biological hazard safety ................................................................................................................................ 66
Safety, Electromagnetic compatibility (EMC), and Environmental standards ..................................... 67
Documentation and support ....................................................................................... 69
Obtaining support ......................................................................................................................................... 69
2 Qubit™ 4 Fluorometer User Guide

About this guide
Overview This user guide describes how to operate the Qubit™ 4 Fluorometer.
User The guides listed below are available with the Qubit™ 4 Fluorometer.
documentation
Guide Pub. No.
Qubit 4 Fluorometer User Guide
™
MAN0017209
Qubit 4 Fluorometer Quick Reference Card (QRC)
™
MAN0017210
Additional resources are available on the Qubit™ Technical Resources page. Go to

thermofisher.com/qubit to access protocols, application notes, and tutorials.
Text and keyboard Text and keyboard conventions used in the Qubit™ 4 Fluorometer User Guide are
conventions listed below. For safety alert words and symbols used in Thermo Fisher Scientific
user documentation, see page 4.
Convention Use
Bold Bold text indicates user action. For example:
Click Run.
 Right arrow symbol () indicates a menu choice, and
separates successive commands you execute or select from a
drop-down or shortcut menu. For example:
Select SettingsInstrument settings.
User attention Two user attention words appear in Thermo Fisher Scientific user documentation.
words Each word implies a particular level of observation or action as described below.
Note: Provides information that may be of interest or help but is not

critical to the use of the product.
IMPORTANT! Provides information that is necessary for proper

instrument operation, accurate installation, or safe use of a chemical.

Safety alert words Four safety alert words appear in Thermo Fisher Scientific user documentation at
points in the document where you need to be aware of relevant hazards. Each
alert word—IMPORTANT, CAUTION, WARNING, DANGER—implies a
particular level of observation or action, as defined below:
IMPORTANT! – Provides information that is necessary for proper

instrument operation, accurate installation, or safe use of a chemical.
CAUTION! – Indicates a potentially hazardous situation that, if not

avoided, may result in minor or moderate injury. It may also be used to
alert against unsafe practices.
WARNING! – Indicates a potentially hazardous situation that, if not

avoided, could result in death or serious injury.
DANGER! – Indicates an imminently hazardous situation that, if not

avoided, will result in death or serious injury. This signal word is to be
limited to the most extreme situations.
Except for IMPORTANT! safety alerts, each safety alert word in a Thermo Fisher
Scientific document appears with an open triangle figure that contains a hazard
symbol. These hazard symbols are identical to the hazard symbols that are affixed
to Thermo Fisher Scientific instruments (see “Safety symbols” in Appendix C).
SDSs The Safety Data Sheets (SDSs) for any chemicals supplied by Thermo Fisher
Scientific are available to you free 24 hours a day. For instructions on obtaining
SDSs, see “Safety Data Sheets (SDS)”.
IMPORTANT! For the SDSs of chemicals not distributed by Thermo

Fisher Scientific contact the chemical manufacturer.

1. Product information
Product contents
The Qubit™ 4 Fluorometer is shipped with the components listed below:
Component Quantity
Qubit 4 Fluorometer
™
1 each
Universal Power Cord with 4 adaptor plugs 1 each
(for U.S./E.U./U.K./Australia)
USB drive (includes the user guide) 1 each
Qubit 4 USB cable
™
1 each
Qubit 4 Fluorometer Quick Reference Card (QRC)
™
1 each
Certificate of Conformity (COC) 1 each
Qubit screen cleaning cloth
™
1 each
The complete user guide is also available for download at thermofisher.com/qubit.

See page 6 for the description and specifications of the Qubit™ 4 Fluorometer.
Upon receiving the Examine the instrument carefully for damage incurred during transit. Ensure that
instrument all parts of the instrument, including the accessories listed above, are included with
the product. Damage claims must be filed with the carrier; the warranty does not
cover in-transit damage.
See page 9 for instructions to set up the Qubit™ 4 Fluorometer.
Register your Go to thermofisher.com/qubit to register your instrument. You will be asked to

instrument supply the serial number, your name, and your contact details. Registering your
instrument ensures that you will receive notifications of software upgrades and
information on new assays for use with the Qubit™ 4 Fluorometer.

Product description
Qubit™ 4 The Qubit™ 4 Fluorometer is a benchtop fluorometer that can be used for the
Fluorometer quantitation of DNA, RNA, microRNA, and protein, as well as for the measurement
of RNA integrity and quality using the highly sensitive and accurate fluorescence-
based Qubit™ assays. Additionally, Ion Sphere™ Particle quality can be evaluated on
the Qubit™ 4 Fluorometer using the Ion Sphere™ Quality Control Kit prior to
performing a sequencing run on the Ion Personal Genome Machine™ (PGM™)
Sequencer. You can also use the Qubit™ 4 Fluorometer to directly measure the
fluorescence of samples or to create new assays using the MyQubit software pre-
programmed into the instrument.
Features • Fast and highly accurate quantitation of DNA, RNA, and protein in less than
3 seconds per sample.
• Measure percentage of intact and degraded RNA in the sample in less than
5 seconds per sample.
• High levels of accuracy using only 1–20 µL of sample, even with very dilute
samples.
• Use of dyes selective for dsDNA, RNA, or protein minimizes the effects of
contaminants in the sample.
• Stores results from up to 1000 samples.
• Large, state-of-the-art color touchscreen for easy workflow navigation.
• Graphically displays up to 20 data points for quantitation assays.
• Instrument indicates samples that are in the extended range or out of range in
the graph, as well as in the simple sample output screen.
• Saves sample data as a CSV (comma separated value) file.
• Exports data to a USB drive or directly to your computer via a USB cable.
• On-board Reagent Calculator provides instructions to prepare Qubit™ working
solution using your sample and standard inputs.
• Allows easy definition and saving of assay preferences.
• Instrument user interface can be personalized to show only the frequently used
assays, to add new assays, including user-defined assays created with the
MyQubit software and web tool, and to display in the language of your choice
including English, French, Spanish, Italian, German, simplified Chinese and
Japanese.

Instrument exterior components
Top view
Back view
Touchscreen is the user interface containing the controls for all the functions
needed and displays data from the assays.
Sample chamber is used to load the assay tube containing the sample into the
fluorometer for analysis.
USB cable port (type mini-B) allows you to transfer your data directly to your
computer using the USB cable supplied with the instrument or any other similar
USB cable.
USB drive ports (Type A) allow you to transfer and save data to your computer
using the USB flash drive supplied with the instrument (or any other similar
USB drive) for record keeping and printing purposes.
Power inlet connects the Qubit™ 4 Fluorometer to an electrical outlet using the
supplied power cord and the appropriate plug, based on the electrical outlet
configuration in your country.

Product specifications
Physical Instrument type: Benchtop fluorometer
characteristics Instrument dimensions: 5.4 in (w) × 10 in (l) × 2.2 in (h)
(13.6 cm × 25 cm × 5.5 cm); rectangular shape
Weight: 26.2 oz (743 g)
Operating power: 100–240 VAC, 1.0 A/1.2 A
Frequency: 50/60 Hz
Electrical input: 12 VDC, 2.5 A
Installation site: Indoor use only
Operating temperature: 10–40°C
Operating humidity: 20–80% (non-condensing)
Technical Dynamic range: 5 orders of magnitude

specifications Processing time: ≤5 seconds/sample
Light sources: Blue LED (max ~470 nm)
Red LED (max ~635 nm)
Excitation filters: Blue 430–495 nm
Red 600–645 nm
Emission filters: Green 510–580 nm
Red 665–720 nm
Detectors: Photodiodes; measurement capability from
300–1000 nm
Calibration type: 2- or 3-point standard
Tube type: 0.5-mL Real Time PCR (polypropylene) tubes
Warm-up time: <35 seconds
USB drive Capacity: 4 Gigabyte

2. Getting started
Set up the Qubit™ 4 Fluorometer
Set up the The Qubit™ 4 Fluorometer is a stand-alone instrument that does not require
instrument connection to a computer.
1. After unpacking the instrument, place the instrument on a flat, level, dry
surface.
2. Plug one end of the supplied power cord into the Qubit™ 4 Fluorometer.
3. Attach the appropriate plug adaptor to the other end of the power cord.
4. Plug the power cord into the electrical outlet.
Note: Ensure the plug of power adaptor remains accessible to allow

disconnection.
5. The instrument automatically powers on, first displaying the splash screen,
and then the Home screen.
6. To power down the Qubit™ 4 Fluorometer, unplug it.
IMPORTANT! Use the power cord plug adapter supplied with the
instrument that is appropriate for the electrical outlet configuration in your
country. Powering the instrument with an unapproved power cord may
damage the instrument.
Home screen When the instrument is powered on, the Home

screen is automatically displayed.
From the Home screen, you can:
• Select one of the assays: dsDNA, RNA, oligo
(ssDNA), protein, or Ion Sphere™.
• Select the Fluorometer mode (the instrument
behaves like a mini-fluorometer).
• Access saved data.
• Configure instrument settings.
• Use the Reagent Calculator to determine the
exact volumes of Qubit™ buffer and reagent
required to prepare the Qubit™ working
solution.

About Instrument The About Instrument screen displays information about your Qubit™ 4 Fluorometer,
screen including the currently installed software version. To access the About Instrument
screen:
1. On the Home screen, press Settings.
2. On the Settings screen, press About Instrument to display the About
Instrument screen.
3. Press Done, Cancel, or Back ( ) to return to the Settings screen.

Optional: Configure instrument settings
Introduction You can configure the following instrument settings for the Qubit™ 4 Fluorometer:
• Sleep mode (page 12)
• Brightness (page 12)
• Date/Time (page 13)
• Reset instrument (page 14)
• Language (page 15)
Access the 1. On the Home screen, press Settings.

Instrument settings 2. On the Settings screen, press Instrument settings to display the
screen Instrument settings screen.

Adjust the sleep The Qubit™ 4 Fluorometer has a sleep mode (i.e., automatic standby) that is
mode triggered by inactivity. The system default is 10 minutes of inactivity before the
instrument goes into sleep mode. To adjust this time:
1. On the Instrument settings screen (page 11), press Sleep mode to display the
Sleep mode screen.

2. Enter the time in minutes allowed before the instrument goes into sleep mode
by pressing the minutes field, then using the number pad to select a value. The
software requires a minimum of 1 minute and a maximum of 60 minutes.
3. Press Done to save the changes and return to the Instrument settings screen.
Press Cancel or Back ( ) to return to the Instrument settings screen without
saving the changes.
Adjust screen 1. On the Instrument settings screen (page 11), press Brightness to display the
brightness Brightness screen.

2. Move the slider button up or down to adjust the brightness of the display.
3. Press Done to save the changes and return to the Instrument settings screen.
Press Cancel or Back ( ) to return to the Instrument settings screen without
saving the changes.

Adjust the date and The date and time are preset when you receive the instrument. To adjust the date
time and time:
1. On the Instrument settings screen (page 11), press Date/Time.

2. Select a date format, select a time format, then press Next.
3. Enter the date and time:
a. Press a date field (day, month, or year),
then use the number pad to select a value.
b. Press a time field (hours or minutes),
then use the number pad to select a value.
c. Select AM or PM.
4. Press Done to save the changes and return to
the Instrument settings screen.
Press Cancel or Back ( ) to return to the
Instrument settings screen without saving the
changes.

Reset function The Reset function returns the Qubit™ 4 Fluorometer to its default factory
settings, and erases all saved data, user–defined instrument settings, and
custom assays.
IMPORTANT! The reset function is not reversible.
To return the instrument to its default factory settings:

1. On the Instrument settings screen (page 11), press Reset instrument to display
the Reset Qubit™ 4 screen.

2. Press Reset. After the reset is complete, the Home screen is displayed. All
data, user–defined instrument settings, and custom assays are removed.
Press Cancel or Exit ( ) to return to the Instrument settings screen without
saving the changes.

Change the display You can change the language that the Qubit™ 4 Fluorometer displays to English
language (default), French, German, Italian, Spanish, simplified Chinese, and Japanese.
1. On the Instrument settings screen (page 11), press Language to display the
Language screen.
2. Select a language, then press Next.

3. Press Yes to confirm the change and return to the Instrument settings screen.
Press Cancel or Exit ( ) to return to the Instrument settings screen without
saving the changes.

Guidelines for using the Qubit™ 4 Fluorometer
Recommendations To obtain the best results, follow the recommendations below. For more
information, see “Critical Qubit™ Assay considerations”, page 57.
• Do not operate the instrument in direct sunlight.
• Wear gloves during sample handling.
• Use the instrument at room temperature only (22–28ºC).
• Bring all kit reagents to room temperature and insert all assay tubes into the
instrument only for as much time as it takes for the instrument to measure the
fluorescence.
• Do not hold the assay tubes in your hand before performing a measurement.
• Make sure that you have calibrated the Qubit™ 4 Fluorometer using the
appropriate standards.
• Incubate the tubes for the Qubit™ DNA and RNA assays for 2 minutes after
mixing the sample or standard with the working solution.
• Incubate the tubes for the Qubit™ protein assays for 15 minutes after mixing
the sample or standard with the working solution.
• If you are performing multiple readings of a single tube, remove the tube
from the instrument and let it equilibrate to room temperature for 30 seconds
before taking another reading.
Note: Multiple readings of RNA samples is not recommended.
• Visit thermofisher.com/qubit for additional application notes, technical notes,
citations, software updates, and a list of validated Qubit™ assays that have
been tested using the Qubit™ 4 Fluorometer.
Assay tubes for the Only thin-wall, clear 0.5-mL PCR tubes are appropriate for use in the Qubit™ 4
Qubit™ 4 Fluorometer. Acceptable tubes include Qubit™ assay tubes (Cat. No. Q32856,
500 tubes). The minimum assay volume must be 200 µL for an accurate read.
Fluorometer

3. Perform assays
Overview
This section provides instructions for using the Reagent Calculator, running new
calibration standards or for using the last calibration, and for reading the samples
using a Qubit™ assay kit.
Materials needed • A Qubit™ assay kit appropriate for quantifying your samples (see page 59 for
available Qubit™ assay kits and ordering information)
• DNA, RNA, or protein samples
• Qubit™ assay tubes or other appropriate 0.5-mL assay tubes
• Appropriate standards for the assay you are performing
Note: For instructions on the preparation of these standards, see the

instructions that accompany the assay you are using or the Qubit™ 4
Fluorometer Quick Reference Card (QRC) (Pub. No. MAN0017210).
• (Optional) USB drive or USB cable for data transfer, supplied with the
instrument or available separately

Optional: Use Reagent Calculator to prepare Qubit™ Working Solution
Introduction Use the on-board Reagent Calculator to quickly determine the correct amount of
Qubit™ dye and buffer required to make the appropriate amount of Qubit™
Working Solution required to prepare your samples and standards.
Use the Reagent 1. On the Home screen, press Reagent Calculator.

Calculator
2. Enter the total number of samples and standards that you will be running on
the Qubit™ 4 Fluorometer.
3. Optional: Select Include overage if you want to include an additional tube in

the total calculated volume.

4. Press Enter to calculate the amount of Qubit™ dye and buffer required to
prepare the Qubit™ Working Solution with these inputs.
Note: You can change the total number of tubes that you plan to run or the
overage selection on this screen.
5. Press Done to return to the Home screen to run your Qubit™ assay.

Calibrate assays on the Qubit™ 4 Fluorometer
Introduction For each assay, you have the choice to run new standards for calibrating the assay
on the Qubit™ 4 Fluorometer or to use the values from the previous calibration (for
more information, see “Qubit™ 4 Fluorometer”, page 58).
Read new 1. On the Home screen, select the assay type for which you wish to read new
standards for standards.
calibration To go to the second page of available assays, swipe the screen to the right. To
return to the first page, swipe the screen to the left.
2. Select the desired assay.
Note: The software displays the available assays for the assay type
you selected in step 1. The example in step 2 shows the available
assays for the dsDNA assay type.

3. If you have already performed a calibration for
the selected assay, the software prompts you to
choose between reading new standards and
running samples using the previous
calibration. Press Read standards.
Note: To apply the previous calibration to your sample readings,

press Run samples. The software prompts you to insert the assay
tube containing sample. See “Read samples”, page 24.
4. At the prompt, insert Standard #1 into the sample chamber and press Read
standard. Be sure to use the Standard #1 appropriate for the assay you are
performing. The reading takes approximately 3 seconds.
5. At the prompt, insert Standard #2 into the

sample chamber and press Read standard.
Be sure to use the Standard #2 appropriate for
the assay you are performing.
6. For Qubit™ protein and RNA IQ assays only: At
the prompt, insert Standard #3 into the sample
chamber and press Read standard.
7. The calibration is complete after Standard #2 is
read (or after Standard #3 is read for the
Qubit™ protein or RNA IQ assay). The
software displays the results.

Calibration results • For Qubit™ quantitation assays: If the calibration is successful, the software
displays the Read standard screen with the Fluorescence vs. Concentration graph.
In the Fluorescence vs. Concentration graph, the standard data points are
connected by a line and open circles represent correct standards.
• For the RNA IQ assay: If the calibration is
successful, the software displays the
Ready for samples message.
• If the calibration is not successful, the software displays the Calibration error
message (page 23).
Note: The Read standard screen displays the raw fluorescence values for
Standard #1 and Standard #2 (and Standard #3, if applicable). These values
can assist you in making a judgment regarding the calibration results.
For the Qubit™ dsDNA BR, Qubit™ dsDNA HS, Qubit™ ssDNA, Qubit™
microRNA, Qubit™ RNA HS, Qubit™ RNA BR, Qubit™ RNA XR, and
Qubit™ protein assays, the reading given by Standard #2 should be at least
ten times higher than that of Standard #1.
For the Qubit™ protein assay, the reading given by Standard #3 should be
at least 40% higher than that of Standard #2.
For the Qubit™ RNA IQ assay, the instrument verifies the calibration
parameters at each stage of the three point calibration process, confirming
the appropriate response of the assay to the standards provided in the kit.
If any issues arise during calibration, the instrument will guide you to
appropriate actions to correct the issue.

Calibration error If you receive the “Calibration error” message,
you can re-run the standards:
1. In the Error screen, press OK.
2. Review the Read standard screen (see Note on
page 22).
3. If you wish to re-run the standards, or run
new standards, press Read standards, then
repeat the calibration procedure (beginning
on page 18).
Note: For the RNA IQ assay, specific standards can be re-run depending
on the calibration error. The error message provides guidance on how to
correct the calibration error.

Read samples
Before you begin • Calibrate the Qubit™ 4 Fluorometer as described on page 18. (Run the
appropriate standards or accept the values from the previous calibration.)
• Prepare the samples. Refer to the instructions provided with the assay.
Note: Incubate the samples for the appropriate amount of time after
mixing them with the working solution (2 minutes for the Qubit™ DNA
and RNA assays, 15 minutes for the Qubit™ protein assay).
Read samples 1. In the Read standard (for Qubit™ quantitation assays) or Ready for samples
screen (for Qubit™ RNA IQ assay), press Run samples.
2. In the Sample volume screen, select the sample volume and units for the Qubit™
quantitation assays or the Qubit™ RNA IQ assay:
a. Press the + or – buttons on the wheel to select the sample volume added
to the assay tube (between 1 and 20 µL).
b. For the Qubit™ quantitation assays, select the units for the output sample
concentration from the dropdown menu.

Note: In the RNA IQ assay, there are no units associated with the RNA IQ
value (i.e., RNA IQ#) and only sample volume is required.

3. Insert a sample tube into the sample chamber, close the lid, and then press
Read tube. The reading takes approximately 3 seconds for the quantitation
assays and approximately 5 seconds for the quality assays.
4. The software displays the results. See “Results screen” on page 26.
Results screen for quantitation Results screen for quality

assays assays
Read multiple To read multiple samples for the same assay:

samples 1. Remove the current sample, and insert a new sample.
2. To change the sample volume, swipe right or press the left arrow.
3. Press Read tube.
4. Repeat step 2 (page 24) and step 3 (page 25).

Results
Results screen – The Results screen displays the results of the sample run.
Sample • If the results are within the assay’s range, the concentration values are displayed.
quantitation The top value (in large font) is the concentration of the original sample. The
bottom value is the dilution concentration (the concentration of the sample in the
tube inserted into the Qubit™ 4 fluorometer).
• If the results are outside of the assay’s range, an “Out of Range” message is
displayed.
• To return to the sample volume screen, swipe right or press the left arrow.

• To view the Fluorescence vs. Concentration graph, swipe left or press the
right arrow. In the graph:
Open circles represent correct standards.
The large gray circle represents the most recent sample.
Blue circles represent samples that fall within the assay’s core range.
Yellow circles represent samples that fall within the assay’s extended
range.
Red circles represent samples or standards that fall outside the assay’s
range.
Single sample Multiple samples
Out of range high Out of range low
• To return to the previous screen, swipe right or press the left arrow.
Note: The Qubit™ 4 Fluorometer automatically stores numeric data from

all reads, but does not store graphic data.

Results screen – The Results screen displays the results of the sample run.
Sample quality • If the results are within the assay’s range, the sample quality values are
displayed. The result presented in the circle (i.e., RNA IQ#) is the total value
for the RNA sample integrity and quality, which is the calculated percentage
of large and small RNA in the sample.
The RNA IQ# is based on a scale of 1–10, similar to other RNA quality scores.
A small RNA IQ# in the assay indicates that the sample is comprised of mainly
small RNA and a larger RNA IQ# indicates that the sample consists of mainly
large RNA or structured RNA (mRNA, tRNA, rRNA).
The actual percentages of small or degraded RNA and large or intact RNA in
the sample are displayed below the RNA IQ#.
Measurement error If the results are outside of the assay’s range, a “Measurement error” message is
displayed.
Measurement error – Sample Measurement error – Sample

concentration too low concentration too high

Fluorometer mode
Introduction You can use the Qubit™ 4 Fluorometer as a mini-fluorometer by selecting the
Fluorometer mode.
The Fluorometer mode allows you to choose the excitation light source (blue LED
or red LED) while reading fluorescence in both the green and far-red emission
channels (for the blue LED) or in the far-red emission channel only (for the red LED).
The reading is in raw fluorescence units (RFU).
Read sample in 1. On the Home screen, press Fluorometer.

Fluorometer mode
2. On the Choose excitation screen, select Blue (470 nm) or Red (635 nm).

3. Insert the sample, then press Read tube.
4. For Blue excitation, the Qubit™ 4 Fluorometer displays both the green
emission and the far red emission of your sample. For Red excitation, the
Qubit™ 4 Fluorometer displays only the far red emission of your sample.
Blue (470 nm) excitation Red (635 nm) excitation
Read multiple To read multiple samples in the fluorometer mode:

samples in 1. Remove the current sample, and insert a new sample.
Fluorometer mode 2. Press Read tube.

Ion Sphere™ Assay
Ion Sphere™ Assay The Ion Sphere™ assay on the Qubit™ 4 Fluorometer enables quick and easy
assessment of Ion Sphere™ Particles (ISPs) prior to performing a sequencing run on
the Ion Personal Genome Machine™ (PGM™) Sequencer using the Ion Sphere™
Quality Control Kit.
All ISPs bind a complimentary, green-fluorescent Alexa Fluor™ 488 dye-labeled
oligonucleotide, whereas only those beads that are template positive bind a
complementary red-fluorescent Alexa Fluor™ 647 dye-labeled oligonucleotide. The
Qubit™ 4 Fluorometer measures the fluorescence emission of each dye conjugate
and a Microsoft Excel™ file template is used to calculate the percentage of template-
positive ISPs from the ratio of the Alexa Fluor™ 647 dye signal to the
Alexa Fluor™ 488 dye signal. This quality-control step using the Qubit™
Fluorometer determines the likelihood of a successful sequencing run, ultimately
saving time and expense during subsequent sequencing.
Note: For more information about the Ion Sphere™ Quality Control Kit
(Cat. No. 4468656), go to thermofisher.com and search for the catalog
number.

4. Manage data
Introduction
The Qubit™ 4 Fluorometer can save data for up to 1000 samples.
For the saved data, the instrument allows you to:
• View detailed data for each sample (page 32).
• Rename data files (page 35).
• Save data as a CSV (comma separated value) file, and export the CSV file to a
USB drive or directly to your computer (page 36).
• Delete data files (page 39)
View detailed sample data

View detailed 1. From the Concentration, Graph, RNA IQ results, or Home screen, press Data.
sample data

2. On the Export data screen, press the data set of interest.
A Data screen displaying a list of data entries for that data set appears. To
view additional data entries that do not fit in the screen, scroll up or down.
Data screen for quantitation assays Data screen for quality assays
3. To reverse the order of the data entries, press the blue chevron above the
sample number column.

4. To view the sample details, press the sample of interest. A Data details screen
opens.
Data details for quantitation assays Data details for quality assays

Rename data files
Rename data files 1. On the Concentration, Graph, RNA IQ results, or Home screen, press Data.
2. On the Export data screen, select the data set of interest.
3. From the list of data entries for the selected data set, press the sample of
interest to open the Data details screen.
Data screen for quantitation assays Data screen for quality assays
4. On the Data details screen, press the Sample # field (indicated by the red
arrow), enter the new name using the keyboard that appears, then press Enter.

Export data
Introduction The Qubit™ 4 Fluorometer is designed for standalone use; it does not require an
external computer. However, to archive data and generate reports, you can export
the numeric data stored in the CSV file to a computer either by using the USB
drive or by saving directly to the computer using the USB cable. You can then
import the file into any spreadsheet program.
Export data using 1. Insert the USB drive into the Qubit™ 4 Fluorometer.
the USB drive 2. On the Concentration, Graph, RNA IQ results, or Home screen, press Data.
3. On the Export data screen, check the selection box to the left of each data set
you wish to export.
4. To save only individual data entries from a data set, press the data set of
interest, and then check the selection box to the left of the samples you wish
to export.

5. Press Export to export the data. The numeric data is automatically saved as a
CSV file.
6. Transfer the USB drive to the USB drive port on your computer. You can open
the CSV file using any spreadsheet program.
Export data directly Data files may also be exported from the Qubit instrument to a computer using a
™
to a computer USB cable such as the one provided with the Qubit™ instrument. The USB cable
must remain connected to both the Qubit instrument and the computer during
™
this process.
Note: The Windows® XP operating system requires the installation of a

driver. The driver and installation instructions are available for download
from Qubit Technical Resources at thermofisher.com/qubit.
To export data directly to a computer:

1. Connect the Qubit™ instrument to the computer using the USB cable.
2. From the computer, access the Qubit™ 4 Fluorometer as an external device.
3. Access the files saved on the Qubit™ instrument using the operating system’s
normal file browsing menus.
4. Copy the desired files to the computer.
Note: Files cannot be exported directly to an external computer using the

Export workflow on the Qubit™ instrument.

Information saved
to the CSV file
Note: For the RNA IQ assay, there is no original sample concentration,

Qubit™ tube concentration or dilution factor. Instead, the results file
contains % large and % small RNA information.

Delete data
Delete data files 1. On the Concentration, Graph, RNA IQ results, or Home screen, press Data.
2. On the Export data screen, check the selection box to the left of each data set
you wish to delete.
To delete only individual data entries from a data set, press the data set of
interest, and then check the selection box to the left of the samples you wish
to delete.
3. Press Delete. A warning screen appears.
4. Press Delete to permanently delete the sample data or data set.

Press Cancel to return to the screen previously viewed without deleting any
data.

5. Manage, import, and create assays
Overview
The Qubit™ 4 Fluorometer allows you to personalize the instrument’s user
interface to hide and show (unhide) assays or folders and to move them to
different locations. In addition, you can add custom MyQubit assays by importing
them from our website at thermofisher.com/qubit or create new assays using the
MyQubit software and web tool.
Manage assays
Manage assays The Manage assays function allows you to hide and show (unhide) assays or folders
function and to move them to different locations.
1. To access the Manage assays function, press Settings on the Home
screen.
2. On the Settings screen, press Manage assays to open the Manage assays screen.
From the Manage assays screen, you can select Show/hide assays (page 41) or
Move assays (page 43).

Show/Hide assays
Show/Hide all 1. From the Settings screen, press Manage assays.
assays within the 2. On the Manage assays screen, press Show/hide assays.
assay folder The software displays a list of the existing assay folders available on the
instrument. Each assay folder contains individual assays.
3. Select the assay folder containing the assays you wish to show or hide.
The software displays a list of existing individual assays within the selected
assay folder and the controls for showing and hiding them.
4. To hide all of the assays in the assay folder, swipe the Assay folder On/Off
switch located to the right of the assay folder name to the Off position (to the
left).
To show all of the assays in the assay folder, swipe the Assay folder On/Off
switch to the On position (to the right).
5. Press the Back button ( ) to save the changes and return to the previous
screen, or press Done to save the changes and return to the Settings screen.

Show/Hide 1. From the Settings screen, press Manage assays.
individual assays 2. On the Manage assays screen, press Show/hide assays.
The software displays a list of the existing assay folders available on the
instrument. Each assay folder contains individual assays.
3. Select the assay folder containing the assays you wish to show or hide.
The software displays a list of existing individual assays within the selected
assay folder and the controls for showing and hiding them.
4. To hide an individual assay, swipe the Assay On/Off switch located to the
right of the assay to the Off position while keeping the Folder On/Off switch
in the On position.
To show an individual assay, swipe the respective Assay On/Off switch to
the On position while keeping the Folder On/Off switch in the On position.
5. Press the Back button ( ) to save the changes and return to the previous
screen, or press Done to save the changes and return to the Settings screen.

Move assays
Move assay folders/ 1. From the Settings screen, press Manage assays.
individual assays on 2. On the Manage assays screen, press Move assays.
the Home screen The software displays the Manage assays screen with available assay folders
and individual assays, and activates the move function.
3. Press and hold on the desired assay folder or individual assay to detach it
from its current position, then drag it to its new location.
To move the selected object to a different Home screen page, drag it up or
down to the desired screen.
4. Release the drag to drop the selected assay folder or individual assay in its
new location.
5. Press the Back button ( ) to save the changes and return to the Manage
assays screen.

Move assays 1. From the Settings screen, press Manage assays.
between folders 2. On the Manage assays screen, press Move assays.
The software displays the Manage assays screen with available assay folders
and individual assays, and activates the move function.
3. Press the desired assay folder to open the folder’s assay screen.
4. Press and hold the individual assay to detach it and drag it over the Home
screen icon ( ).
5. Release the drag to drop the selected assay to the Home screen.
6. Press the Home button ( ) to return to the Home screen.
In the Home screen, you can press and drag the selected assay to another
assay folder or location as described in “Move assay folders/ individual
assays on the Home screen”, page 43.
assays screen.
Move assays within 1. From the Settings screen, press Manage assays.
folders 2. On the Manage assays screen, press Move assays.
3. Press the desired assay folder to open the folder’s assay screen.
4. Press and hold the individual assay to detach it, and drag and drop it to its
new location in the folder.
assays screen.

Import assays
MyQubit assay files You can add pre-existing MyQubit assays to your Qubit™ 4 Fluorometer by
downloading the assay files from thermofisher.com/qubit, then importing the files
to the instrument from a USB drive or from an external computer via a USB cable.
Note: MyQubit assay files have the file extension .qbt.
Import assays from 1. To import one or more new assays, go to thermofisher.com/qubit and
a USB drive download the MyQubit assay files (.qbt file) you wish to install to the root
directory of a USB drive.
Do not download the .qbt files to a folder in the USB drive.
2. Insert the USB drive containing the new assay files into the USB drive port of
the Qubit™ 4 Fluorometer.
3. Go to the Settings screen and press Import new assay. The instrument
searches the USB drive for assay files and the Import new assay screen displays
the names of the assays found in the USB drive.

4. Press the assays you wish to import to select. Touching the selected assay a
second time deselects it. You can select multiple assays for import.

5. Press Next. The Import new assay screen displays the name of the assay being
imported (or the first assay, if multiple assays were selected) and lists the
destination folders where you can save it.
Press the Back button ( ) or Cancel to return to the Settings screen without
importing the assays.
Note: Each assay folder can contain up to 9 individual assays. The

Home screen can contain up to 36 assays or folders.
6. Select the destination folder for the new assay and press Save. The Verification
screen opens (see Step 9, page 47).
Alternatively, press New folder to create a new destination folder (see Step 8,
page 47).
Press the Back button ( ) or Cancel to abort the import process and return to
the Settings screen.

7. In the New folder screen, press the New folder text field. The keyboard opens.
Using the keyboard, enter the name of the new destination folder. You can
use up to 11 characters; spaces at the beginning or the end of the name are not
recognized.
Press Enter, then press Done to return to the Import new assay – Where screen.
The newly created folder will appear on the list of folders.
Select the new destination folder, then press Save. The Verification screen
opens (see Step 9, page 48).
8. In the Verification screen, press Done to complete the import process.

If importing only one assay, you will be returned to the Home screen.
If importing multiple assays, you will be returned to the Import new assay
screen and prompted to select the destination folder for the next assay in your
import queue (see Step 10, page 48).

9. Select the destination folder for the next assay in your import queue, then
press Save.
Repeat this process until you have imported all the assays you have selected
in Step 4 (page 45).
Once all the assays you have selected are imported successfully, the
Verification screen opens.
10. Press Done to complete the import process and return to the Home screen.

Import assays from When the Qubit™ 4 Fluorometer is connected to a computer via a USB cable,
a computer MyQubit .qbt assay files can be transferred directly from the computer to the
instrument.
1. Go to thermofisher.com/qubit and download the MyQubit assay files (.qbt
file) you wish to install.
2. Connect the Qubit™ 4 Fluorometer from the USB cable port to the computer
using a mini-B USB cable. The Qubit™ 4 Fluorometer should be recognized as
an external device by the computer.
3. Copy and paste or click-drag the .qbt files you wish to import to the Qubit™
instrument window on your computer.
Note: The assays will not be visible on the Qubit™ 4 Fluorometer until
you perform the next step.
4. Go to the Settings screen on the Qubit™ 4 Fluorometer and press Import new
assay. The Import new assay screen displays the names of the assays found on
the computer.

5. Follow Steps 4–11 of the import procedure described in “Import assays from a
USB drive”, page 45.
Note: The USB cable must remain connected to both the Qubit™ 4
Fluorometer and the computer for the assay to be imported.

Create your own assay for the Qubit™ 4 Fluorometer
Create a MyQubit All Qubit™ 4 Fluorometers are pre-loaded with MyQubit software, which allows
assay you to create new applications for the Qubit™ 4 Fluorometer using parameters
uploaded to the instrument via a USB drive, without changing the existing assays.
Fluorometer mode allows you to use the Qubit™ 4 Fluorometer with any reagent
or assay compatible with the optical settings of the instrument. In this way, the
device can be used as a mini-fluorometer. With the data gathered in the
Fluorometer mode, personalized, custom assays can be created using the guided
webtool and the MyQubit EZGuide available at thermofisher.com/qubit.
Note: For complete instructions on creating your own assay and access to
the web tool, go to thermofisher.com/qubit.

6. Instrument maintenance
Maintenance and cleaning
Maintenance The Qubit™ 4 Fluorometer does not need regular maintenance. To troubleshoot
problems with the instrument, contact Technical Support (page 69).
• Do not perform any repairs or service on the Qubit™ 4 Fluorometer to avoid
damaging the instrument.
• Do not expose the Qubit™ 4 Fluorometer to direct sunlight.
CAUTION! Never disassemble or service the instrument yourself. Do not

remove any covers or parts that require the use of a tool. Unauthorized
repairs may damage the instrument or alter its functionality, which may
void your warranty. Contact your local distributor to arrange for service.
Clean the Qubit™ 4 We recommend that you clean the Qubit™ 4 Fluorometer periodically to prevent the
Fluorometer buildup of dust and dirt that might reduce its performance and cause contamination.
CAUTION! To avoid electrical shock, always disconnect the power cable

before cleaning or decontaminating the instrument.
IMPORTANT! Using a cleaning or decontaminating method other than

that specified by the manufacturer may result in damage to the instrument.
• Clean the surface of the Qubit™ 4 Fluorometer with a damp cloth.

• To clean the touchscreen, disconnect the power cable, and clean the touchscreen
with a soft cloth lightly moistened with LCD (liquid crystal display) cleansing
detergent.
• Cleaning the screen with excessive force can damage the touchscreen. Wipe the
screen dry immediately.
• Do not use abrasive cleaning solutions or material to prevent the touchscreen
from getting scratched.
• To disinfect the instrument, disconnect the power cable from the Qubit™ 4
Fluorometer and clean the instrument, including the touchscreen, with a soft
cloth lightly moistened with 70% ethanol, 70% isopropanol, or 10% bleach
(0.6% sodium hypochlorite).
• The cloth included with the instrument is not recommended for use with
ethanol or isopropanol.
• Ensure that the cleaning solution does not enter the power button, the power
inlet, the sample port, or the USB drive ports.
• Never pour or spray any liquids directly on the instrument to avoid electrical
shock when the instrument is plugged in.

Software updates
Update the To update the Qubit™ 4 Fluorometer with the latest software from Thermo Fisher
software Scientific:
1. Download the latest software to a USB drive or to your computer from
thermofisher.com/qubit.
2. If using a USB drive, insert the USB drive into the instrument.
If using a computer, connect the Qubit™ instrument to the computer using a
USB cable. The Qubit™ Fluorometer will be recognized as an external device
by the computer.
Note: The connection between the computer and the Qubit™ instrument
must be maintained until the transfer and update (described in the next
steps) are complete.
a. On your computer, find the Qubit™ software update file that you wish to
upload.
b. Copy and paste or click-drag the software file to the Qubit™ instrument
drive. This saves the software file to the root directory of your Qubit™
instrument; however, the software file transfer will not be visible on the
Qubit™ instrument.
4. On the Settings screen, press Update software. The instrument searches the
USB drive or the computer for the update.
Note: If the USB drive is not inserted into the USB drive port or the
instrument does not recognize the USB drive, a warning message is
displayed.
To proceed with the software update, insert the correct USB drive into
the instrument, then press Close.

5. When the appropriate files are detected, the Software update screen is
displayed. Press Update to update the software.
6. When prompted, press Restart to complete the software update.

Device verification test
Perform Device The device verification test checks the internal components of the Qubit™ 4
verification test Fluorometer. Perform the device verification test when a problem with the
instrument is suspected. It is not necessary to perform the verification test on a
regular basis.
2. On the Settings screen, press Device verification test. Verification test screen
opens.
3. On the Verification test screen, press Start test.
4. When the test is complete, the software displays the error status.
• If no errors are found, press Close to return to the Settings screen.
• If errors are found, a Verification test failed message appears. Verify that
the test was run with the lid closed. If the Verification test failed message
persists with the lid closed, contact Technical Support for help (page 69).

Appendix A: Troubleshooting
Troubleshooting
Handling samples • The calibration standards included in the Qubit™ microRNA, Qubit™ RNA HS,
Qubit™ RNA XR, Qubit™ RNA IQ, and Qubit™ RNA BR Assay Kits are high-
quality RNA standards. The integrity and concentration of these standards is
critical to the optimal performance of the Qubit™ RNA assays. We highly
recommend treating the rRNA standards as you would any other precious
RNA. Use appropriate RNAse-free handling techniques, including RNAse-
free gloves, pipette tips, and tubes. Keep the tube lids closed whenever
possible; do not press the pipet to the inside wall of the tube when
withdrawing a sample. Return the RNA standards to –80°C as soon as
possible after use.
• Ensure that the assay tubes are at room temperature at the time the reading is
taken. Do not hold assay tubes in your hand and do not leave assay tubes in
the Qubit™ 4 Fluorometer for longer than it takes to read the fluorescence. See
“Assay temperature”, page 58.
• Be careful not to spill sample into the sample chamber. Promptly wipe any
spills.
• The Qubit™ assays are very sensitive and even small amounts of material
from a previous sample may result in errors. Use a clean 0.5-mL PCR tube for
each reading.
• The tube must be clean and dry on the outside when taking readings.
Moisture and condensation on the tube surface can lead to reading errors.
• Minute bubbles in samples will cause errors in readings. Be sure not to
introduce bubbles into samples. Slight tapping on the tube wall or brief
centrifugation will often help dissipate bubbles.
High reading • The sample is out of range. Use a sample that is less concentrated.
• For Qubit™ quantitation assays, view the
Fluorescence vs. Concentration graph in the
Results screen to confirm that the values for
the samples fall between the values of the
standards (page 27).
• Ensure that the lid is closed while reading
standards and samples.
• Prepare samples and standards according to
the instructions in the Qubit™ assay kit you
are using.
• Ensure that the assay is performed entirely at
room temperature.

Low reading • The sample is out of range. Use a sample that is more concentrated or use a
lower dilution (for example, 20 µL in 180 µL instead of 10 µL in 190 µL).
• For Qubit™ quantitation assays, view the
Fluorescence vs. Concentration graph in the
Results screen to confirm that the values for
the samples fall between the values of the
standards (page 27).
• Ensure that you have prepared the Qubit™
working solution correctly (1:200 dilution
using the buffer provided in the kit).
• Ensure that you have prepared the standard
tubes correctly (10 µL of each standard in
190 µL of Qubit™ working solution).
• Ensure that the standard and sample tubes
are filled to 200 µL.
• Protect the Qubit™ reagent and working
solutions from light.
• Select the correct Qubit™ 4 Fluorometer assay for the Qubit™ assay you are
performing and calibrate the fluorometer correctly. Standards must be used
in the correct order.
• Ensure that the assay is performed entirely at room temperature.

Critical Qubit™ Assay considerations
How the Qubit™ 4 The Qubit™ 4 Fluorometer generates concentration data based on the relationship
Fluorometer between the two standards used in calibration (three for the Qubit™ protein
assay). The plot below shows the line corresponding to the curve-fitting
calculates
algorithm (a modified Hill plot) used in the calculation of concentration data for
concentration the Qubit™ RNA HS assay. For reference, the positions of the standards and a set
of data points from an actual experiment are shown superimposed onto the line.
This plot demonstrates that the curve-fitting algorithm gives accurate values for
quantitation.
Figure 1. The curve-fitting algorithm used to determine concentration in the Qubit™ RNA HS
assay. Data for other Qubit™ quantitation assays are generated by similar algorithms.
Incubation time To allow the Qubit™ assay to reach maximum fluorescence, incubate the tubes for
the DNA and RNA assays for 2 minutes after mixing the sample or standard with
the working solution. After this incubation period, the fluorescence signal is stable
for 3 hours at room temperature for all nucleic acid assays except the Qubit™
ssDNA assay, which is stable for up to 30 minutes.
The Qubit™ protein assay requires 15 minutes of incubation for a stable signal. For
greatest accuracy in the protein assay, the incubation time of the samples should
be within 10 minutes of the incubation time of the standards.
Photobleaching of The Qubit™ DNA and protein exhibit high photostability in the Qubit™ 4
Qubit™ reagents Fluorometer, showing <0.3% drop in fluorescence after 9 readings and <2.5%
drop in fluorescence after 40 readings. It is important to remember, however, that
if the assay tube remains in the Qubit™ 4 Fluorometer for multiple readings, a
temporary reduction in fluorescence will be observed as the solution increases in
temperature (see Figure 2 in “Assay temperature”, page 58). The RNA assays
including the RNA IQ assay should only be read once.
Note that the temperature inside the Qubit™ 4 Fluorometer may be as much as
3°C above room temperature after 1 hour. For this reason, if you want to perform
multiple readings of a single tube, remove the tube from the instrument and let it
equilibrate to room temperature for 30 seconds before taking another reading.

Assay temperature The Qubit™ assays were designed to be performed at room temperature (22–28°C),
and temperature fluctuations can influence the accuracy of the assay.
To minimize temperature fluctuations, store all kit reagents at room temperature
and insert all assay tubes into the Qubit™ 4 Fluorometer only for as much time as
it takes for the instrument to measure the fluorescence, because the Qubit™ 4
Fluorometer can raise the temperature of the assay solution significantly, even
over a period of a few minutes. Do not hold the assay tubes in your hand before a
measurement, because holding the tubes warms the solution and results in a low
reading.
Figure 2. Effect of temperature on the Qubit™ dsDNA BR assay. Qubit™ dsDNA HS, Qubit™
ssDNA, Qubit™ RNA HS, Qubit™ RNA XR, Qubit™ RNA IQ, and Qubit™ protein assays show
similar sensitivities over the same range.
Qubit™ 4 For each assay, you have the choice to run a new calibration or to use the values
Fluorometer from the previous calibration. As you first use the instrument, you perform a new
calibration each time. As you become familiar with the assays, the instrument,
calibration
your pipetting accuracy, and significant temperature fluctuations within your
laboratory, you can determine the level of comfort you have using the calibration
data stored from the last time the instrument was calibrated. Remember also that
the fluorescence signal in the tubes containing the standards and the samples is
stable for not longer than 3 hours. See Figure 1 in “How the Qubit™ 4 Fluorometer
calculates concentration” (page 57) for an example of the calibration curve used to
generate the quantitation results.

Appendix B: Ordering information
Qubit™ 4 Fluorometer and accessories
The following products can be used with the Qubit™ 4 Fluorometer and are
available separately from Thermo Fisher Scientific. For more information, visit
thermofisher.com or contact Technical Support (page 69).
Product Quantity Cat. No.

Qubit 4 Fluorometer
™
1 each Q33226
Qubit 4 Starter Kit
™
1 kit Q33227
Qubit 4 NGS Starter Kit
™
1 kit Q33228
Qubit RNA IQ Starter Kit
™
1 kit Q33229
Qubit 4 USB Flash Drive
™
1 each Q46009
Qubit 4 Fluorometer International Power Supply
™
1 each A36204
(replacement)
Qubit™ Assay Tubes 500 tubes Q32856
Qubit RNA IQ Assay Kit
™
75 assays Q33221
275 assays Q33222
Qubit™ RNA XR Assay Kit *20–1,000 ng* 100 assays Q33223
500 assays Q33224
Qubit™ RNA HS Assay Kit *5–100 ng* 100 assays Q32852
500 assays Q32855
Qubit™ ssDNA Assay Kit *1–200 ng* 100 assays Q10212
Qubit dsDNA BR Assay Kit *2–1,000 ng*
™
100 assays Q32850
500 assays Q32853
Qubit™ dsDNA HS Assay Kit *0.2–100 ng* 100 assays Q32851
500 assays Q32854
Qubit™ 1X dsDNA HS Assay Kit 100 assays Q33230
500 assays Q33231
Qubit™ Protein Assay Kit *0.25–5 µg* 100 assays Q33211
500 assays Q33212
Qubit™ microRNA Assay Kit *0.5–100 ng* 100 assays Q32880
500 assays Q32881
Qubit™ dsDNA HS Assay - Lambda DNA Standard 5 mL Q33233
Qubit RNA IQ Assay - RNA Standards
™
1 set Q33235
Qubit™ RNA XR Assay - RNA Standard 5 each Q33236

Appendix C: Safety
Symbols on instruments
Electrical symbols The following table describes the electrical symbols that may be displayed.
Symbol Description
Indicates a terminal that can receive or supply alternating current or
voltage.
Safety symbols The following table describes the safety symbols that may be displayed. Each
symbol may appear by itself or in combination with text that explains the relevant
hazard (see “Safety labels on instruments”). These safety symbols may also appear
next to DANGERS, WARNINGS, and CAUTIONS that occur in the text of this and
other product-support documents.
Symbol Description
Indicates that you should consult the manual for further information and to
proceed with appropriate caution.
Indicates the presence of an electrical shock hazard and to proceed with
appropriate caution.
Environmental The following symbol applies to all Thermo Fisher Scientific electrical and
symbols electronic products placed on the European market after August 13, 2005.
Symbol Description
Do not dispose of this product 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).
European Union customers:
Call your Customer Service representative for equipment pick-up and
recycling. See thermofisher.com for a list of customer service offices in
the European Union.

Safety labels on instruments
The following CAUTION, WARNING, and DANGER statements may be
displayed on Thermo Fisher Scientific instruments in combination with the safety
symbols described in the preceding section.
Hazard
English Français
symbol
CAUTION! Hazardous chemicals. Read the ATTENTION! Produits chimiques dangereux.
Safety Data Sheets (SDSs) before handling. Lire les fiches techniques de sûreté de
matériels avant toute manipulation de produits.
CAUTION! Hazardous waste. Refer to SDS(s) ATTENTION! Déchets dangereux. Lire les
and local regulations for handling and disposal. fiches techniques de sûreté de matériels et la
régulation locale associées à la manipulation et
l’élimination des déchets.
DANGER! High voltage. DANGER! Haute tension.
WARNING! To reduce the chance of electrical AVERTISSEMENT! Pour éviter les risques
shock, do not remove covers that require tool d’électrocution, ne pas retirer les capots dont
access. No user-serviceable parts are inside. l’ouverture nécessite l’utilisation d’outils.
Refer servicing to Thermo Fisher Scientific L’instrument ne contient aucune pièce
qualified service personnel. réparable par l’utilisateur. Toute intervention
doit être effectuée par le personnel de service
qualifié venant de chez Thermo Fisher
Scientific.

General instrument safety
WARNING! PHYSICAL INJURY HAZARD. Use this product only as
specified in this document. Using this instrument in a manner not specified
may result in personal injury or damage to the instrument.
Operating the Ensure that anyone who operates the instrument has:
instrument • Received instructions in both general safety practices for laboratories and
specific safety practices for the instrument.
• Read and understood all applicable Safety Data Sheets (SDSs). See “Safety
Data Sheets (SDS)”.
Safety precautions Do not install the instrument in heavy humidity such as a greenhouse or an
incubator to avoid a danger of electric shock. If water or other material enters the
instrument, the adaptor, or power inlet, disconnect the power cord and contact a
service person. For operating environment, refer to “Product specifications”
(page 8).
• Do not press the main plug or power cord with wet hands.
• Always ensure that the power supply input voltage matches the voltage
available in your location.
• Do not install the instrument on a slant or a place prone to vibrations, which
induces the risk of instrument malfunction or damage of the instrument.
• Plug the power cord firmly into the wall outlet and the instrument.
• To avoid potential shock hazard, make sure that the power cord is properly
grounded.
• Be sure to position the equipment such that it is easy to disconnect the
instrument.
• If the instrument is broken or dropped, disconnect the power cord and contact
technical services. Do not disassemble the instrument.
• Use only authorized accessories (adaptor, power cord, and USB drive).
• For operating environment, see “Product specifications” (page 8).
• If the instrument emits smoke, disconnect the power cord from the wall outlet
and contact technical services.
Cleaning or CAUTION! Using cleaning or decontamination methods other than those

decontaminating recommended by the manufacturer may compromise the safety or quality
the instrument of the instrument.
Removing covers or CAUTION! PHYSICAL INJURY HAZARD The instrument is to be

parts of the serviced only by trained personnel or vendor specified in the user guide.
instrument Do not remove any covers or parts that require the use of a tool to obtain
access to moving parts.

Chemical safety
Chemical hazard WARNING! CHEMICAL HAZARD. Before handling any chemicals, refer
warning to the Safety Data Sheet (SDS) provided by the manufacturer, and observe
all relevant precautions.
WARNING! CHEMICAL STORAGE HAZARD. Never collect or store

waste in a glass container because of the risk of breaking or shattering.
Reagent and waste bottles can crack and leak. Each waste bottle should be
secured in a low-density polyethylene safety container with the cover
fastened and the handles locked in the upright position. Wear appropriate
eyewear, clothing, and gloves when handling reagent and waste bottles.
General safety To minimize the hazards of chemicals:

guidelines • Read and understand the Safety Data Sheets (SDSs) provided by the chemical
manufacturer before you store, handle, or work with any chemicals or
hazardous materials. (See “Safety Data Sheets (SDS)”, page 69)
• Minimize contact with chemicals. Wear appropriate personal protective
equipment when handling chemicals (for example, safety glasses, gloves, or
protective clothing). For additional safety guidelines, consult the SDS.
• Minimize the inhalation of chemicals. Do not leave chemical containers open.
Use only with adequate ventilation (for example, fume hood). For additional
safety guidelines, consult the SDS.
• Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the
manufacturer’s cleanup procedures as recommended in the SDS.
• Comply with all local, state/provincial, or national laws and regulations
related to chemical storage, handling, and disposal.

Chemical waste safety
Chemical waste CAUTION! HAZARDOUS WASTE. Refer to Safety Data Sheets (SDSs)
hazard and local regulations for handling and disposal.
Chemical waste To minimize the hazards of chemical waste:

safety guidelines • Read and understand the Safety Data Sheets (SDSs) provided by the
manufacturers of the chemicals in the waste container before you store,
handle, or dispose of chemical waste. (See “Safety Data Sheets (SDS)”,
page 69)
• Provide primary and secondary waste containers. (A primary waste container
holds the immediate waste. A secondary container contains spills or leaks
from the primary container. Both containers must be compatible with the
waste material and meet federal, state, and local requirements for container
storage.)
• Minimize contact with chemicals. Wear appropriate personal protective
equipment when handling chemicals (for example, safety glasses, gloves, or
protective clothing). For additional safety guidelines, consult the SDS.
• Minimize the inhalation of chemicals. Do not leave chemical containers open.
Use only with adequate ventilation (for example, fume hood). For additional
safety guidelines, consult the SDS.
• Handle chemical wastes in a fume hood.
• After emptying the waste container, seal it with the cap provided.
• Dispose of the contents of the waste tray and waste bottle in accordance with
good laboratory practices and local, state/provincial, or national
environmental and health regulations.
Waste disposal If potentially hazardous waste is generated when you operate the instrument, you
must:
• Characterize (by analysis, if necessary) the waste generated by the particular
applications, reagents, and substrates used in your laboratory.
• Ensure the health and safety of all personnel in your laboratory.
• Ensure that the instrument waste is stored, transferred, transported, and
disposed of according to all local, state/provincial, and/or national
regulations.
IMPORTANT! Radioactive or biohazardous materials may require special

handling, and disposal limitations may apply.

Electrical safety
DANGER! ELECTRICAL SHOCK HAZARD. Severe electrical shock can
result from operating the Qubit™ 4 Fluorometer without its instrument
panels in place. Do not remove instrument panels. High‐voltage contacts
are exposed when instrument panels are removed from the instrument.
Power DANGER! ELECTRICAL HAZARD. Grounding circuit continuity is vital

for the safe operation of equipment. Never operate equipment with the
grounding conductor disconnected.
DANGER! ELECTRICAL HAZARD. Use properly configured and

approved line cords for the voltage supply in your facility.
DANGER! ELECTRICAL HAZARD. Plug the system into a properly

grounded receptacle with adequate current capacity.
Overvoltage rating The Qubit™ 4 Fluorometer has an installation (overvoltage) category of II, and is
classified as portable equipment.

Biological hazard safety
WARNING! BIOHAZARD. Biological samples such as tissues, body
fluids, and blood of humans and other animals have the potential to
transmit infectious diseases. Follow all applicable local, state/provincial,
and/or national regulations. Wear appropriate protective eyewear,
clothing, and gloves. Read and follow the guidelines in these publications.
ATTENTION! BIOHAZARD. Les échantillons biologiques tels que les

tissus, les fluides corporels et le sang des humains et d’autres animaux ont
la possibilité de transmettre des maladies infectieuses. Suivre tous les
règlements municipaux, provinciaux/provincial et / ou nationales en
vigueur. Porter des lunettes de protection approprié, des vêtements et des
gants.
In the U.S.:
• U.S. Department of Health and Human Services guidelines published in
Biosafety in Microbiological and Biomedical Laboratories
(stock no. 017-040-00547-4;
www.cdc.gov/OD/ohs/biosfty/bmbl4/bmbl4toc.htm)
• Occupational Safety and Health Standards, Bloodborne Pathogens
(29 CFR§1910.1030;
www.access.gpo.gov/nara/cfr/waisidx_01/29cfr1910a_01.html)
• Your company’s/institution’s Biosafety Program protocols for working
with/handling potentially infectious materials.
• Additional information about biohazard guidelines is available at:
www.cdc.gov
In the EU:
• Check your local guidelines and legislation on biohazard and biosafety
precaution, and the best practices published in the World Health Organisation
(WHO) Laboratory Biosafety Manual, third edition
www.who.int/csr/resources/publications/biosafety/WHO_CDS_CSR_LYO_
2004_11/en/

Safety, Electromagnetic compatibility (EMC), and Environmental
standards
This section provides information on:
• U.S. and Canadian safety and EMC standards
• European safety, EMC, and Environmental standards
• Australian EMC standards
• China RoHS Standards
U.S. and Canadian The Qubit™ 4 Fluorometer has been tested to and complies with standard:
Safety standards UL 61010-1/CAN/CSA-C22.2 No. 61010-1, “Safety Requirements for Electrical
Equipment for Measurement, Control, and Laboratory Use, Part 1: General
Requirements.”
UL 61010-2-081/CAN/CSA-C22.2 No. 61010-2-081, “Safety Requirements for
Electrical Equipment for Measurement, Control, and Laboratory Use, Part 2-081:
Particular Requirements for Automatic and Semi-Automatic Laboratory
Equipment for Analysis and Other Purposes.”
U.S. EMC standard This instrument has been tested to and complies with standard 47 CFR FCC
Part 15 “Radio Frequency Devices”; Subpart B “Unintentional Radiators”.
Note: This equipment has been tested and found to comply with the limits for a
Class B digital device, pursuant to part 15 of the FCC Rules. These limits are
designed to provide reasonable protection against harmful interference in a
residential installation. This equipment generates, uses, and can radiate radio
frequency energy and, if not installed and used in accordance with the
instructions, may cause harmful interference to radio communications. However,
there is no guarantee that interference will not occur in a particular installation. If
this equipment does cause harmful interference to radio or television reception,
which can be determined by turning the equipment off and on, the user is
encouraged to try to correct the interference by one or more of the following
measures:
- Reorient or relocate the receiving antenna.
- Increase the separation between the equipment and receiver.
- Connect the equipment into an outlet on a circuit different from that to which
the receiver is connected.
- Consult the dealer or an experienced radio/TV technician for help.
Canadian EMC This instrument has been tested to and complies with standard ICES-001,
standard “Industrial, Scientific and Medical (ISM) Radio Frequency Generators.”

European Safety, Safety
EMC, and This instrument meets European requirements for safety (Low Voltage Directive
Environmental 2014/35/EU). This instrument has been tested to and complies with standards:
standards IEC/EN 61010-1:2010, “Safety Requirements for Electrical Equipment for
Measurement, Control and Laboratory Use, Part 1: General Requirements.”
IEC/EN 61010-2-081:2015, "Safety requirements for electrical equipment for
measurement, control, and laboratory use - Part 2-081: Particular requirements for
automatic and semi-automatic laboratory equipment for analysis and other
purposes."
EMC
This instrument meets European requirements for emission and immunity (EMC
Directive 2014/30/EU). This instrument has been tested to and complies with
standards:
EN 61326-1:2013 Class B, “Electrical Equipment for Measurement, Control and
Laboratory Use – EMC Requirements.”
EN 61000-3-2:2014, “Electromagnetic compatibility (EMC) — Part 3 – 2: Limits —
Limits for harmonic current emissions (equipment input current ≤16 A per phase).”
EN 61000-3-3:2013, “Electromagnetic compatibitity (EMC) — Part 3 – 3: Limits –
Limitation of voltage changes, voltage fluctuations and flicker in public low-
voltage supply systems, for equipment with rated current ≤ 16 A per phase and not
subject to conditional connection (IEC 61000‒3‒3:2008).”
Restriction of Hazardous Substance (RoHS)
This instrument meets European requirements RoHS Directive 2011/65/EU.
This instrument has been tested to and complies with standard EN 50581:2012,
“Technical documentation for the evaluation of electrical and electronic products
with respect to restriction of hazardous substances.”
Waste of Electrical and Electronic Equipment (WEEE)

This instrument meets European requirement WEEE Directive 2012/19/EU.
Australian EMC This instrument has been tested to and complies with standard AS/NZS CISPR 11,
standards “Limits and Methods Measurement of Electromagnetic Disturbance Characteristics
of Industrial, Scientific, and Medical (ISM) Radio‐frequency Equipment.”
China RoHS This instrument does not contain any hazardous substances above the limit and
standards complies with China RoHS standards:
GB/T 26572-2011, “Requirements on Concentration Limits for Certain Restricted
Substances in Electrical and Electronic Products”
SJ/T 11364-2014, "Marking for the Restricted Use of Hazardous Substances in
Electronic and Electrical Products"

Documentation and support
Obtaining support
Technical support Visit thermofisher.com/support for the latest in services and support, including:
• Worldwide contact telephone numbers
• Product support, including:
- Product FAQs
- Software, patches, and updates
- Training for many applications and instruments
• Order and web support
• Product documentation, including:
- User guides, manuals, and protocols
- Certificates of Analysis
- Safety Data Sheets (SDSs; also known as MSDSs)
Safety Data Sheets Safety Data Sheets (SDSs) are available at thermofisher.com/support.
(SDS)
IMPORTANT! For SDSs for reagents and chemicals from other
manufacturers, contact the manufacturer.
Limited product Life Technologies Corporation and/or its affiliate(s) warrant their products as set
warranty forth in the Life Technologies’ General Terms and Conditions of Sale found on
Life Technologies’ website at www.thermofisher.com/us/en/home/global/terms-
and-conditions.html. If you have any questions, please contact Life Technologies
at www.thermofisher.com/support.
IMPORTANT! Wiping the Qubit™ 4 Fluorometer computer (i.e., erasing

the hard drive to remove all programs, files, and the operating system)
voids the product warranty.

thermofisher.com/support | thermofisher.com/askaquestion
thermofisher.com
09 April 2018

Qubit 4 Fluorometer: Catalog Number Q33226

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Qubit™ 4 Fluorometer

Catalog Number Q33226

Publication Number MAN0017209

For Research Use Only. Not for use in diagnostic procedures.

Information in this document is subject to change without notice.

Revision Date Description

© 2018 Thermo Fisher Scientific Inc. All rights reserved.

ii Qubit™ 4 Fluorometer User Guide

Qubit™ 4 Fluorometer User Guide 1

2 Qubit™ 4 Fluorometer User Guide

Additional resources are available on the Qubit™ Technical Resources page. Go to

Note: Provides information that may be of interest or help but is not

IMPORTANT! Provides information that is necessary for proper

Qubit™ 4 Fluorometer User Guide 3

IMPORTANT! – Provides information that is necessary for proper

CAUTION! – Indicates a potentially hazardous situation that, if not

WARNING! – Indicates a potentially hazardous situation that, if not

DANGER! – Indicates an imminently hazardous situation that, if not

IMPORTANT! For the SDSs of chemicals not distributed by Thermo

4 Qubit™ 4 Fluorometer User Guide

The complete user guide is also available for download at thermofisher.com/qubit.

Register your Go to thermofisher.com/qubit to register your instrument. You will be asked to

Qubit™ 4 Fluorometer User Guide 5

6 Qubit™ 4 Fluorometer User Guide

Qubit™ 4 Fluorometer User Guide 7

Technical Dynamic range: 5 orders of magnitude

USB drive Capacity: 4 Gigabyte

8 Qubit™ 4 Fluorometer User Guide

Note: Ensure the plug of power adaptor remains accessible to allow

Home screen When the instrument is powered on, the Home

Qubit™ 4 Fluorometer User Guide 9

3. Press Done, Cancel, or Back ( ) to return to the Settings screen.

10 Qubit™ 4 Fluorometer User Guide

Access the 1. On the Home screen, press Settings.

Qubit™ 4 Fluorometer User Guide 11

12 Qubit™ 4 Fluorometer User Guide

Qubit™ 4 Fluorometer User Guide 13

IMPORTANT! The reset function is not reversible.

To return the instrument to its default factory settings:

14 Qubit™ 4 Fluorometer User Guide

2. Select a language, then press Next.

Qubit™ 4 Fluorometer User Guide 15

16 Qubit™ 4 Fluorometer User Guide

Note: For instructions on the preparation of these standards, see the

Qubit™ 4 Fluorometer User Guide 17

Use the Reagent 1. On the Home screen, press Reagent Calculator.

3. Optional: Select Include overage if you want to include an additional tube in

18 Qubit™ 4 Fluorometer User Guide

Qubit™ 4 Fluorometer User Guide 19

2. Select the desired assay.

20 Qubit™ 4 Fluorometer User Guide

Note: To apply the previous calibration to your sample readings,

5. At the prompt, insert Standard #2 into the

Qubit™ 4 Fluorometer User Guide 21

22 Qubit™ 4 Fluorometer User Guide

Qubit™ 4 Fluorometer User Guide 23

24 Qubit™ 4 Fluorometer User Guide

Results screen for quantitation Results screen for quality

Read multiple To read multiple samples for the same assay: