A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Zhou, Cong ^a   Bowler, Lucas D ^a   Feng, Jianfeng ^b,c  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

^b UNIVERSITY OF WARWICK   (United Kingdom)

^c FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN NEURAL NETWORKS; FRAGMENTATION PATHWAYS; GAS-PHASE FRAGMENTATION; INTENSITY INFORMATION; MACHINE LEARNING APPROACHES; PEPTIDE FRAGMENTATION; PROTEIN IDENTIFICATION; TANDEM MASS SPECTROMETRY;

ALGORITHMS; MASS SPECTROMETRY; NEURAL NETWORKS;

PEPTIDES;

PEPTIDE FRAGMENT; PROTON; PEPTIDE;

ACCURACY; ALGORITHM; ARTICLE; ARTIFICIAL NEURAL NETWORK; BAYES THEOREM; CONTROLLED STUDY; EXPERIMENTAL DESIGN; INFORMATION PROCESSING; MACHINE LEARNING; MOLECULAR LIBRARY; NONHUMAN; PEPTIDE ANALYSIS; PREDICTION; PROTEIN ANALYSIS; RELIABILITY; SIGNAL TRANSDUCTION; SYSTEM ANALYSIS; TANDEM MASS SPECTROMETRY; ARTIFICIAL INTELLIGENCE; METHODOLOGY; PROTEOMICS;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; BAYES THEOREM; NEURAL NETWORKS (COMPUTER); PEPTIDES; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 51249111303     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-325     Document Type: Article

References (29)

1. Chamrad DC Korting G Stuhler K Meyer HE Klose J Bluggel M Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data Proteomics 2004, 4(3):619-628. 10.1002/pmic.200300612 14997485
2. Eng JK McCormack AL Yates JR An Approach to Correlate Tandem Mass Spectra Data of Peptides with Amino Acid Sequences in a Protein Database J Am Soc Mass Spectrom 1994, 5(11):976. 10.1016/1044-0305(94)80016-2
3. Perkins DN Pappin DJ Creasy DM Cottrell JS Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20(18):3551-3567. 10.1002/ (SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 10612281
4. Sadygov RG Yates JR A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases Anal Chem 2003, 75:3792-3798. 10.1021/ ac034157w 14572045
5. Fenyo D Beavis RC A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes Anal Chem 2003, 75:768-774. 10.1021/ac0258709 12622365
6. Havilio M Haddad Y Smilansky Z Intensity-based statistical scorer for tandem mass spectrometry Anal Chem 2003, 75:435-444. 10.1021/ac0258913 12585468
7. Bern M Goldberg D McDonald WH Yates JR 3rd Automatic quality assessment of peptide tandem mass spectra Bioinformatics 2004, 20:i49-i54. 10.1093/ bioinformatics/bth947 15262780
8. Narasimhan C Tabb DL Verberkmoes NC Thompson MR Hettich RL Uberbacher EC MASPIC: Intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence Anal Chem 2005, 77:7581-7593. 10.1021/ac0501745 16316165
9. Wysocki VH Tsaprailis G Smith LL Breci LA Mobile and localized protons: a framework for understanding peptide dissociation J Mass Spectrom 2000, 35(12):1399-1406. 10.1002/ 1096-9888(200012)35:12<1399::AID-JMS86>3.0.CO;2-R 11180630
10. Dongré AR Jones JL Somogyi Á Wysocki VH Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: Evidence for the mobile proton model J Am Soc Mass Spectrom 1996, 118:8365-8374.
11. Tsaprailis G Nair H Somogyi Á Wysocki VH Zhong W Futrell JH Summerfield SG Gaskell SJ Influence of secondary structure on the fragmentation of protonated peptides J Am Chem Soc 1999, 121(22):5142-5154. 10.1021/ja982980h
12. Gu C Tsaprailis G Breci L Wysocki VH Selective gas-phase cleavage at the peptide bond terminal to aspartic acid in fixed-charge derivatives of asp-containing peptides Anal Chem 2000, 72:5804-5813. 10.1021/ac000555c 11128940
13. Tsaprailis G Nair H Zhong W Kuppannan K Futrell JH Wysocki VH A mechanistic investigation of the enhanced cleavage at histidine in the gas-phase dissociation of protonated peptides Anal Chem 2004, 76:2083-2094. 10.1021/ac034971j 15053674
14. Breci LA Tabb DL Yates JR 3rd Wysocki VH Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra Anal Chem 2003, 75:1963-1971. 10.1021/ac026359i 12720328
15. Kapp EA Schutz F Reid GE Eddes JS Moritz RL O'Hair RA Speed TP Simpson RJ Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptides' fragmentation Anal Chem 2003, 75:6251-6264. 10.1021/ac034616t 14616009
16. Schutz F Kapp EA Simpson RJ Speed TP Deriving statistical models for predicting peptide tandem MS product ion intensities Biochem Soc Trans 2003(Pt 6):1479-1483. 14641094
17. Zhang Z Prediction of low-energy collision-induced dissociation spectra of peptides Anal Chem 2004, 76:3908-3922. 10.1021/ac049951b 15253624
18. Zhang Z Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges Anal Chem 2005, 77:6364-6373. 10.1021/ac050857k 16194101
19. Elias JE Gibbons FD King OD Roth FP Gygi SP Intensity-based protein identification by machine learning from a library of tandem mass spectra Nature Biotechnology 2004, 22:214-219. 10.1038/nbt930 14730315
20. Graves PR Haystead TAJ Molecular Biologist's Guide to Proteomics Microbiology and Molecular Biology Reviews 2002, 66:39-63. 10.1128/ MMBR.66.1.39-63.2002
21. Tabb DL Huang Y Wysocki VH Yates JR 3rd Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides Anal Chem 2004, 76:1243-1248. 10.1021/ ac0351163 14987077
22. Savitski MM Kjeldsen F Nielsen ML Garbuzynskiy SO Galzitskaya OV Surin AK Zubarev RA Backbone Carbonyl Group Basicities Are Related to Gas-Phase Fragmentation of Peptides and Protein Folding Angew Chem Int Ed Engl 2007, 46(9):1481-1484. 10.1002/anie.200603881 17211901
23. Huang Y Triscari JM Tseng GC Pasa-Tolic L Lipton MS Smith RD Wysocki VH Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns Anal Chem 2005, 77:5800-5813. 10.1021/ac0480949 16159109
24. Tabb DL Statistical characterization of ion trap tandem mass spectra from doubly charged trypic peptides Anal Chem 2003, 75:1155-1163. 10.1021/ac026122m 12641236
25. Keller A Purvine S Nesvizhskii A Stolyar S Goodlett DR Kolker E Experimental Protein Mixture for Validating Tandem Mass Spectral Analysis OMICS 2002, 6(2):207-212. 10.1089/153623102760092805 12143966
26. Sun S Meyer-Arendt K Eichelberger B Brown R Yen C-Y Old WM Pierce K Cios KJ Ahn NG Resing KA Improved validation of peptide MS/MS assignments using spectral intensity prediction Mol Cell Proteomics 2007, 6:1-17. 10.1074/mcp.M600449-MCP200 17018520
27. Bishop CM Neural networks for pattern recognition Clarendon Press/OUP 1995.
28. MacKay D Bayesian methods for neural networks: Theory and applications Course notes for Neural Networks Summer School 1995. http://www.inference.phy.cam.ac.uk/mackay/BayesNets.html
29. Sauve AC Speed TP Normalization, Baseline Correction and Alignment of High-throughput Mass Spectrometry Data Data proceedings Gensips 2004.