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Mutation-tolerant protein identification by mass-spectrometry

Authors:

Pavel A. Pevzner,

Vlado Dančík,

Chris L. TangAuthors Info & Claims

RECOMB '00: Proceedings of the fourth annual international conference on Computational molecular biology

Pages 231 - 236

https://doi.org/10.1145/332306.332560

Published: 08 April 2000 Publication History

Abstract

Database search in tandem mass spectrometry is a powerful tool for protein identification. High-throughput spectral acquisition raises the problem of dealing with genetic variation and peptide modifications within a population of related proteins. A method that cross-correlates and clusters related spectra in large collections of uncharacterized spectra (i.e from normal and diseased individuals) would be extremely valuable in functional proteomics. This problem is far from being simple since very similar peptides may have very different spectra. We introduce a new notion of spectral similarity that allows one to identify related spectra even if the corresponding peptides have multiple modifications/mutations. Based on this notion we developed a new algorithm for mutation-tolerant database search as well as a method for cross-correlating related uncharacterized spectra. The paper describes this new approach and its applications in functional proteomics.

References

[1]

C. Bartels Fast algorithm for peptide sequencing by mass spectroscopy B;omed. Envsrom. Muss Spectrora, 19:363-368, 1990

[2]

K. Biemann and H. A. Scoble Characterization of tandem mass spectrometry of structural modifications in proteins Science, 237.992-998, 1987

[3]

K R. Clauser, P. R Baker, and A L Burlingame Tile role of accurate mass measurement ( +/- 10ppm) in protein ~dentification strategies employing MS or MS/MS and database searching. Anal. Chem, 71.2871-2882, 1999

[4]

K. R. Clauser, P.R. Baker, and A.L. Burhngame. In ggth ASM$ Conference on Mass Spectrometry and AU~ed Topacs, Portland, Oregon, May 1~-16, page 365, Portland, OR, May 12-16 1996

[5]

V. Danclk, T. Addona, K. O!auser, J Vath, and P.A Pevzner. De novo peptide sequencing v~a tandem mass spectrometry J. Comp. B;ology, 6'327-342, 1999

[6]

V. Dancik and P A. Pevzner. Anti-symmetric path problem in tandem mass-spectrometry (m preparat~or~), 1999

[7]

J Eng, A. McCormack, and J Yules An approach to correlate tandem mass spectral data of peptJdes w~ttJ amino acid sequences in a protein database. J Am Soc. Mass Spectom, 5:976-989, 1994.

[8]

D. Fenyo, J. Qin, and B.T Chair Protein identificat}on using mass spectrometric informatlon Electrophorests, 19 998-1005, 1998

[9]

J. Fernandez-de Cossio, J Gonzales, and V Besada. A computer program to md the sequencing of pep~ides in collision-activated decomposition experiments G'ABIOS, 11:427-434, 1995.

[10]

13 Funarl, N. Rhind, and P. Russell. C:dc25 mitotic inducer targeted by Chkl DNA damage checkpoint kinase $c, ence, 277.1495-1497, 1997.

[11]

A Cooley and N. Packer The importance of co- and posttranslational modifications in proteome projects In W. Wilkins, K Wilhams, R Appei, and D Hochstrasser, editors, Proteome Research: New Front, er$ :n F~nct~onul Genom~cs, pages 65-91. Springer, 1997

[12]

1~. J Johnson and K Bxemann Computer program (seqpep) to aid in the interpretation of high-energy collision tandem mass spectra of peptides B~orr~ed. E~v. Mass Spectrom, t8 945-957, 1989.

[13]

M. Mann and M. Wilm. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem., 66.4390-4399, 1994

[14]

Z. Mulyukov and P.A Pewner Efficiency of mutation-tolerant database search with tandem mass spectra (In preparation), 1999

[15]

A. $hevchenko, M Wilm, and M. Mann. Peptide mass spectrometry for homology searches and cloning of genes. J Protein Chemistry, 5 481-490, 1997

[16]

J A Taylor and R S Johnson. Sequence database searches via de nolo peptide sequencing by tandem mass spectrometry. Rapid Communtcat,ons :n Mass Spectrometry, 11.1067-1075, 1997.

[17]

J Yules, J- Eng, A MeCormack, and D. Sehieltz. Method to correlate tandem mass spectra of modified peptides to amino acid sequences m the protein database Anal. Chem., 67 1426- 1436, 1995

[18]

J. R Yates, J. K Eng, and A L McCormack. Mining genomes Correlating tandem mass-spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal Chem., 67 3202-3210, 1995.

Cited By

Song YChi A(2015)Peptide sequencing via graph path decompositionInformation Sciences: an International Journal10.1016/j.ins.2015.01.003301:C(262-270)Online publication date: 20-Apr-2015
https://dl.acm.org/doi/10.1016/j.ins.2015.01.003
Song Y(2014)A New Parameterized Algorithm for Rapid Peptide SequencingPLoS ONE10.1371/journal.pone.00874769:2(e87476)Online publication date: 14-Feb-2014
https://doi.org/10.1371/journal.pone.0087476
Tan HLeong H(2011)A Parent Mass Filter Algorithm for Peptide Sequencing from Tandem Mass Spectra2011 5th International Conference on Bioinformatics and Biomedical Engineering10.1109/icbbe.2011.5780091(1-4)Online publication date: May-2011
https://doi.org/10.1109/icbbe.2011.5780091
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Mutation-tolerant protein identification by mass-spectrometry
1. Applied computing
  1. Life and medical sciences

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Published In

cover image ACM Conferences

RECOMB '00: Proceedings of the fourth annual international conference on Computational molecular biology

April 2000

329 pages

ISBN:1581131860

DOI:10.1145/332306

Editors:
Ron Shamir
Tel-Aviv Univ., Israel
,
Satoru Miyano
Univ. of Tokyo, Tokyo, Japan
,
Sorin Istrail
Sandia National Labs
,
Pavel Pevzner
Univ. of Southern California
,
Michael Waterman
Univ. of Southern California

Copyright © 2000 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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New York, NY, United States

Publication History

Published: 08 April 2000

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Cited By

Song YChi A(2015)Peptide sequencing via graph path decompositionInformation Sciences: an International Journal10.1016/j.ins.2015.01.003301:C(262-270)Online publication date: 20-Apr-2015
https://dl.acm.org/doi/10.1016/j.ins.2015.01.003
Song Y(2014)A New Parameterized Algorithm for Rapid Peptide SequencingPLoS ONE10.1371/journal.pone.00874769:2(e87476)Online publication date: 14-Feb-2014
https://doi.org/10.1371/journal.pone.0087476
Tan HLeong H(2011)A Parent Mass Filter Algorithm for Peptide Sequencing from Tandem Mass Spectra2011 5th International Conference on Bioinformatics and Biomedical Engineering10.1109/icbbe.2011.5780091(1-4)Online publication date: May-2011
https://doi.org/10.1109/icbbe.2011.5780091
Yu CWang GWu JMao K(2009)Classifying b and y ions in peptide tandem mass spectraProceedings of the 6th international conference on Fuzzy systems and knowledge discovery - Volume 510.5555/1801874.1801883(37-41)Online publication date: 14-Aug-2009
https://dl.acm.org/doi/10.5555/1801874.1801883
Yu CWang GZhai WMao K(2009)A novel scoring strategy for identifying peptide via tandem mass spectraProceedings of the 6th international conference on Fuzzy systems and knowledge discovery - Volume 510.5555/1801874.1801877(8-12)Online publication date: 14-Aug-2009
https://dl.acm.org/doi/10.5555/1801874.1801877
Ning KChong KLeong H(2006)A database search algorithm for identification of peptides with multiple charges using tandem mass spectrometryProceedings of the 2006 international conference on Data Mining for Biomedical Applications10.1007/11691730_2(2-13)Online publication date: 9-Apr-2006
https://dl.acm.org/doi/10.1007/11691730_2
Han YMa BZhang K(2004)An automata approach to match gapped sequence tags against protein databaseProceedings of the 9th international conference on Implementation and Application of Automata10.1007/978-3-540-30500-2_16(167-177)Online publication date: 22-Jul-2004
https://dl.acm.org/doi/10.1007/978-3-540-30500-2_16
Bafna VEdwards NMiller W(2003)On de novo interpretation of tandem mass spectra for peptide identificationProceedings of the seventh annual international conference on Research in computational molecular biology10.1145/640075.640077(9-18)Online publication date: 10-Apr-2003
https://dl.acm.org/doi/10.1145/640075.640077
Edwards NLippert R(2002)Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass SpectrometryAlgorithms in Bioinformatics10.1007/3-540-45784-4_6(68-81)Online publication date: 10-Oct-2002
https://doi.org/10.1007/3-540-45784-4_6
Chen TJaffe JChurch GLengauer T(2001)Algorithms for identifying protein cross-links via tandem mass spectrometryProceedings of the fifth annual international conference on Computational biology10.1145/369133.369177(95-102)Online publication date: 22-Apr-2001
https://dl.acm.org/doi/10.1145/369133.369177
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