Search and decoy: The automatic identification of mass spectra

Methods in Molecular Biology

Volumn 893, Issue , 2012, Pages 445-488

  Eisenacher, Martin ^a   Kohl, Michael ^a   Turewicz, Michael ^a   Koch, Markus Hermann ^a   Uszkoreit, Julian ^a   Stephan, Christian ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

Comparison; Decoy; False Discovery Rate; Identification; Mass Spectra; Protein Ambiguity; Proteomics; Search Engine

Indexed keywords

PROTEOME;

ALGORITHM; ARTICLE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER PROGRAM; HUMAN; INFORMATION PROCESSING; PEPTIDE MAPPING; PROTEIN DATABASE; PROTEOMICS; SEARCH ENGINE; STATISTICAL ANALYSIS; TANDEM MASS SPECTROMETRY;

ALGORITHMS; AUTOMATIC DATA PROCESSING; DATA INTERPRETATION, STATISTICAL; DATABASES, PROTEIN; HUMANS; PEPTIDE MAPPING; PROTEOME; PROTEOMICS; SEARCH ENGINE; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 84864134313     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-885-6_28     Document Type: Article

References (35)

1. Hunt DF, Yates JR 3rd, Shabanowitz J et al (1986) Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci USA 83(17): 6233-6237
2. Eng JK, McCormack AL, Yates JR (1994) An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database. J Am Soc Mass Spectrom 5(11):976-989
3. Perkins DN, Pappin DJ, Creasy DM et al (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18): 3551-3567
4. Colinge J, Masselot A, Giron M et al (2003) OLAV: Towards high-throughput tandem mass spectrometry data identification. Proteomics 3(8):1454-1463
5. Craig R, Beavis RC (2004) TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 20(9):1466-1467
6. Geer LY, Markey SP, Kowalak JA et al (2004) Open mass spectrometry search algorithm. J Proteome Res 3(5):958-964
7. Peng J, Elias JE, Thoreen CC et al (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J Proteome Res 2(1):43-50
8. Cargile BJ, Bundy JL, Stephenson JL Jr et al (2004) Potential for false positive identifications from large databases through tandem mass spectrometry. J Proteome Res 3(5): 1082-1085
9. Elias JE, Haas W, Faherty BK et al (2005) Comparative evaluation of mass spectrometry platforms used in large-scale Proteomics investigations. Nat Methods 2(9):667-675
10. Kapp EA, Schutz F, Connolly LM et al (2005) An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and speci ficity analysis. Proteomics 5(13):3475-3490
11. Reidegeld KA, Eisenacher M, Kohl M et al (2008) An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications. Proteomics 8(6):1129-1137
12. Balgley BM, Laudeman T, Yang L, Song T et al (2007) Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy. Mol Cell Proteomics 6(9): 1599-1608
13. Lam H, Deutsch EW, Aebersold R (2010) Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in Proteomics. J Proteome Res 9(1): 605-610
14. Lam H, Deutsch EW, Eddes JS et al (2007) Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7(5):655-667
15. Seidler J, Zinn N, Boehm ME et al (2010) De novo sequencing of peptides by MS/MS. Proteomics 10(4):634-649
16. Sadygov RG, Cociorva D, Yates JR 3rd (2004) Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book. Nat Methods 1(3):195-202
17. Pappin DJ, Hojrup P, Bleasby AJ (1993) Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol 3(6):327-332
18. Ong SE, Mann M (2005) Mass spectrometrybased Proteomics turns quantitative. Nat Chem Biol 1(5):252-262
19. Silva JC, Gorenstein MV, Li GZ et al (2006) Absolute quantification of proteins by LCMSE: A virtue of parallel MS acquisition. Mol Cell Proteomics 5(1):144-156
20. Ishihama Y, Oda Y, Tabata T et al (2005) Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in Proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 4(9):1265-1272
21. Park CY, Klammer AA, Kall L et al (2008) Rapid and accurate peptide identification from tandem mass spectra. J Proteome Res 7(7): 3022-3027
22. Eng JK, Fischer B, Grossmann J et al (2008) A fast SEQUEST cross correlation algorithm. J Proteome Res 7(10):4598-4602
23. Faherty BK, Gerber SA (2010) MacroSEQUEST: Ef ficient candidate-centric searching and highresolution correlation analysis for large-scale Proteomics data sets. Anal Chem 82(16): 6821-6829
24. Keller A, Eng J, Zhang N et al (2005) A uniform Proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol 1:2005.0017
25. Turewicz M, Deutsch EW (2011) Spectra, chromatograms, Metadata: MzML-the standard data format for mass spectrometer output. Meth Mol Biol 696:179-203
26. Fenyo D, Beavis RC (2003) A method for assessing the statistical signi ficance of mass spectrome try-based protein identifications using general scoring schemes. Anal Chem 75(4):768-774
27. Sadygov RG, Yates JR 3rd (2003) A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal Chem 75(15):3792-3798
28. Keller A, Nesvizhskii AI, Kolker E et al (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74(20): 5383-5392
29. Nesvizhskii AI, Keller A, Kolker E et al (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75(17): 4646-4658
30. Kallberg M, Lu H (2010) An improved machine learning protocol for the identification of correct Sequest search results. BMC Bioinformatics 11:591
31. Klammer AA, Park CY, Noble WS (2009) Statistical calibration of the SEQUEST XCorr function. J Proteome Res 8(4):2106-2113
32. Link AJ, Eng J, Schieltz DM et al (1999) Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17(7):676-682
33. Han DK, Eng J, Zhou HL et al (2001) Quantitative pro filing of differentiationinduced microsomal proteins using isotopecoded af finity tags and mass spectrometry. Nat Biotechnol 19(10):946-951
34. Balgley BM, Laudeman T, Yang L et al (2007) Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy. Mol Cell Proteomics 6(9):1599-1608
35. Pendarvis K, Kumar R, Burgess SC et al (2009) An automated proteomic data analysis work fl ow for mass spectrometry. BMC Bioinformatics 10:S17