Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge

Proteome Science

Volumn 10, Issue 1, 2012, Pages

  Sridhara, Viswanadham ^a   Bai, Dina L ^b   Chi, An ^c   Shabanowitz, Jeffrey ^b   Hunt, Donald F ^b,d   Bryant, Stephen H ^a   Geer, Lewis Y ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b UNIVERSITY OF VIRGINIA   (United States)

^c MERCK RESEARCH LABORATORIES   (United States)

^d UNIVERSITY OF VIRGINIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; DISSOCIATION; ELECTRON TRANSFER DISSOCIATION; FILTER DESIGN; NOISE; PEPTIDE ANALYSIS; PEPTIDE LIBRARY; PROTEIN PROCESSING; SENSITIVITY ANALYSIS;

EID: 84856787141     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-10-8     Document Type: Article

References (25)

1. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003, 422:198-207.
2. Kelleher NL. Top-down proteomics. Anal Chem 2004, 76:197A-203A.
3. Schroeder MJ, Shabanowitz J, Schwartz JC, Hunt DF, Coon JJ. A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry. Anal Chem 2004, 76:3590-3598.
4. Swaney DL, McAlister GC, Wirtala M, Schwartz JC, Syka JE, Coon JJ. Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Anal Chem 2007, 79:477-485.
5. Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 2004, 101:9528-9533.
6. Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH. Open mass spectrometry search algorithm. J Proteome Res 2004, 3:958-964.
7. Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20:1466-1467.
8. Yates JR, Eng JK, McCormack AL, Schieltz D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem 1995, 67:1426-1436.
9. Tabb DL, Fernando CG, Chambers MC. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res 2007, 6:654-661.
10. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
11. Zubarev RA, Zubarev AR, Savitski MM. Electron capture/transfer versus collisionally activated/induced dissociations: solo or duet?. J Am Soc Mass Spectrom 2008, 19:753-761.
12. Falth M, Savitski MM, Nielsen ML, Kjeldsen F, Andren PE, Zubarev RA. Analytical utility of small neutral losses from reduced species in electron capture dissociation studied using SwedECD database. Anal Chem 2008, 80:8089-8094.
13. Sun RX, Dong MQ, Song CQ, Chi H, Yang B, Xiu LY, Tao L, Jing ZY, Liu C, Wang LH, et al. Improved peptide identification for proteomic analysis based on comprehensive characterization of electron transfer dissociation spectra. J Proteome Res 2010, 9:6354-6367.
14. Geer LY, Bai DL, Shabanowitz J, Kowalak JA, Markey SP, Bryant SH, Hunt DF. An algorithm for sequence searching of peptide spectra generated via electron transfer dissociation. J Am Soc Mass Spec 2005, 16:S2-S169.
15. Chalkley RJ, Medzihradszky KF, Lynn AJ, Baker PR, Burlingame AL. Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry. Anal Chem 2010, 82:579-584.
16. Liu X, Shan B, Xin L, Ma B. Better score function for peptide identification with ETD MS/MS spectra. BMC Bioinformatics 2010, 11(Suppl 1):S4.
17. Coon JJ, Ueberheide B, Syka JE, Dryhurst DD, Ausio J, Shabanowitz J, Hunt DF. Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc Natl Acad Sci USA 2005, 102:9463-9468.
18. Sadygov RG, Hao Z, Huhmer AF. Charger: combination of signal processing and statistical learning algorithms for precursor charge-state determination from electron-transfer dissociation spectra. Anal Chem 2008, 80:376-386.
19. Carvalho PC, Cociorva D, Wong CC, Carvalho MD, Barbosa VC, Yates JR. Charge prediction machine: tool for inferring precursor charge states of electron transfer dissociation tandem mass spectra. Anal Chem 2009,
20. Sharma V, Eng JK, Feldman S, von Haller PD, MacCoss MJ, Noble WS. Precursor charge state prediction for electron transfer dissociation tandem mass spectra. J Proteome Res 2010, 9:5438-5444.
21. Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci USA 2007, 104:2193-2198.
22. Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 2007, 4:207-214.
23. Good DM, Wenger CD, McAlister GC, Bai DL, Hunt DF, Coon JJ. Post-acquisition ETD spectral processing for increased peptide identifications. J Am Soc Mass Spectrom 2009, 20:1435-1440.
24. Sweet SM, Jones AW, Cunningham DL, Heath JK, Creese AJ, Cooper HJ. Database search strategies for proteomic data sets generated by electron capture dissociation mass spectrometry. J Proteome Res 2009, 8:5475-5484.
25. Na S, Paek E, Lee C. CIFTER: automated charge-state determination for peptide tandem mass spectra. Anal Chem 2008, 80:1520-1528.