The probability distribution for a random match between an experimental-theoretical spectral pair in tandem mass spectrometry

Journal of Bioinformatics and Computational Biology

Volumn 3, Issue 2, 2005, Pages 455-476

  Fridman, Tema ^a   Razumovskaya, Jane ^b   Verberkmoes, Nathan ^b   Hurst, Greg ^a   Protopopescu, Vladimir ^a   Xu, Ying ^c  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

Author keywords

Database search; Mass spectrometry; Tandem

Indexed keywords

ALBUMIN; ALCOHOL DEHYDROGENASE; CARBONATE DEHYDRATASE; HEMOGLOBIN ALPHA CHAIN; HEMOGLOBIN BETA CHAIN; LYSOZYME; MYOGLOBIN;

ACCURACY; ALGORITHM; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; INTERMETHOD COMPARISON; NONHUMAN; PEPTIDE ANALYSIS; PERFORMANCE; PROBABILITY; TANDEM MASS SPECTROMETRY; THEORETICAL MODEL; VALIDATION PROCESS;

ALGORITHMS; MASS SPECTROMETRY; MODELS, CHEMICAL; MODELS, STATISTICAL; PEPTIDE MAPPING; PEPTIDES; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; STATISTICAL DISTRIBUTIONS;

EID: 17644368549     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720005001120     Document Type: Article

References (32)

1. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G, Functional organization of the Yeast proteome by systematic analysis of protein complexes, Nature 415:141-147, 2002.
2. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R, Quantitative analysis of complex protein mixtures using isotope-coded affinity tags, Nat Biotechnol 17:994-999, 1999.
3. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M, Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry, Nature 415 180-183, 2002.
4. Hunt DF, Yates III JR, Shabanowitz J, Winston S, Hauer CR, Protein sequencing by tandem mass spectrometry, Proc Natl Acad Sci USA 83:6233-6237, 1986.
5. Jungblut P, Thiede B, Protein identification from 2-D gels by MALDI mass spectrometry, Mass Spectrom Rev 16:145-162, 1997.
6. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates III JR, Direct analysis of protein complexes using mass spectrometry, Nat Biotechnol 17:676-682, 1999.
7. Mann M, Hendrickson RC, Pandey A, Analysis of proteins and proteomes by mass spectrometry, Annu Rev Biochem 70:437-473, 2001.
8. Peng J, Gygi SP, Proteomics: The move to mixtures, J Mass Spec 36:1083-1091, 2001.
9. Shevchenko A, Wilm M, Vorm O, Mann M, Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels, Anal Chem 68 850-858, 1996.
10. Washburn MP, Wolters D, Yates III JR, Large-scale analysis of the yeast proteome by multidimensional protein identification technology, Nat Biotechnol 19:242-247, 2001.
11. Aebersold R, Mann M, Mass spectrometry-based proteomics, Nature 422(6928): 198-207, 2003. Review.
12. Eng JK, McCormack AL, Yates III JR, An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database, J Am Soc Mass Spectrom 5:976-989, 1994.
13. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS, Probability-based protein identification by searching sequence databases using mass spectrometry data, Electrophoresis 20(18):3551-3567, 1999.
14. Hansen BT, Mason DE, Jones JA, Liebler DC, SALSA: An algorithm for detection of modified peptides by automated evaluation of their CID spectra in LC-tandem MS analyses, Anal Chem 73:1676-1683, 2001.
15. Bafna V, Edwards N, SCOPE: A probabilistic model for scoring tandem mass spectra against a peptide database, Bioinformatics 17 Suppl 1):S13-21, 2001.
16. Sonar http://65.219.84.5/ProteinId.html.
17. http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/algo/ms/ omssa/omssacl.cpp
18. http://www.thegpm.org/TANDEM/index.html; http://www.proteome.ca/x-bang/ tandem/tandem.html
19. Pappin D, Hojrup P, Bleasby A, (1994) http://www.hgmp.mrc.ac.uk/ Bioinformatics/Webapp/mowse/mowsedoc.html
20. Huang Y, Wysocki VH, Tabb DL, Yates III JR, The influence of histidine on cleavage C-terminal to acidic residues in doubly protonated tryptic peptides, Int Journ Mass Spectr 219:233-244, 2002.
21. Tsaprailis G, Nair H, Somogyi A, Wysocki VH, Zhong W, Futrell JH, Summerfield SG, Gaskell SJ, Influence of secondary structure on the fragmentation of protonated peptides, J Am Chem Soc 121 5142-5154, 1999.
22. Tsaprailis G, Somogyi A, Nikolaev EN, Wysocki VH, Refining the model for selective cleavage at acidic residues in arginine-containing protonated peptides, Int Journ Mass Spec 195/196:467-479, 2000.
23. Mann M, Useful tables of possible and probable peptide masses in 43rd ASMS Conference on Mass Spectrometry and Allied Topics, Am Soc Mass Spectr, Atlanta.
24. Sadygov R, Yates III J, A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases, Anal Chem 75:3792-3798, 2003.
25. Roepstorff P, Fohlman J, Proposal for a common nomenclature for sequence ions in mass spectra of peptides, Biomed Mass Spectrom 11:601, 1984.
26. Biemann K, Contributions of mass-spectrometry to peptide and protein structure, Biomed Environ Mass Spectrom 16:99-111, 1988.
27. Keller A, Purvine S, Nesvizhskii A, Stolyar S, Goodlett D, Kolker E, Experimental protein mixture for validating tandem mass spectral analysis, OMICS 6(2):207-212, 2002.
28. Keller A, Nesvizhskii AI, Kolker E, Aebersold R, Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search, Anal Chem 74(20):5383-92, 2002.
29. Moore R, Young M, Lee T, Qscore: An algorithm for evaluating SEQUEST database search results, J Am Soc Mass Spectrom 13 (4):378-86, 2002.
30. Nolan D, Speed T, Mathematical statistics through applications, Stat Labs, Springer Texts in Statistics, Springer, p. 107, 2001.
31. Dancik V, Addona TA, Clauser KR, Vath JE, Pevzner PA, De novo sequencing via tandem mass spectrometry, J Comput Biol 6 327-342, 1999.
32. Fridman T, Day R, Razumovskaya J, Xu D, Gorin AA, Probability profiles - novel approach in mass spectrometry de novo sequencing, CSB2003 Conference Proceedings, Stanford University 11-14 August 2003, pp. 415-418, 2003.