Verification of automated peptide identifications from proteomic tandem mass spectra

Nature Protocols

Volumn 1, Issue 5, 2006, Pages 2213-2222

  Tabb, David L ^a,b   Friedman, David B ^a   Ham, Amy Joan L ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PEPTIDE;

ANIMAL; ARTICLE; CHEMISTRY; HELICOBACTER PYLORI; METHODOLOGY; MICROVILLUS; MOUSE; PROTEOMICS; TANDEM MASS SPECTROMETRY;

ANIMALS; BACTERIAL PROTEINS; HELICOBACTER PYLORI; MICE; MICROVILLI; PEPTIDES; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 34548449808     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2006.330     Document Type: Article

References (37)

1. Eng, J.K., McCormack, A.L. & Yates, J.R. III. 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).
2. Perkins, D.N., Pappin, D.J., Creasy, D.M. & Cottrell, J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567 (1999).
3. Washburn, M.P., Wolters, D. & Yates, J.R. III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247 (2001).
4. Daikoku, T. et al. Proteomic analysis identifies immunophilin FK506 binding protein 4 (FKBP52) as a downstream target of Hoxa10 in the periimplantation mouse uterus. Mol. Endocrinol. 19, 683-697 (2005).
5. Wysocki, V.H., Tsaprailis, G., Smith, L.L. & Breci, L.A. Mobile and localized protons: A framework for understanding peptide dissociation. J. Mass Spectrom. 35, 1399-1406 (2000).
6. Paizs, B. & Suhai, S. Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 24, 508-548 (2005).
7. Huang, Y., Wysocki, V.H., Tabb, D.L. & Yates, J.R. III. The influence of histidine on cleavage C-terminal to acidic residues in doubly protonated tryptic peptides. Int. J. Mass Spectrom. 219, 233-244 (2002).
8. Schlosser, A., Pipkorn, R., Bossemeyer, D. & Lehmann, W.D. Analysis of protein phosphorylation by a combination of elastase digestion and neutral loss tandem mass spectrometry. Anal. Chem. 73, 170-176 (2001).
9. Reid, G.E., Roberts, K.D., Kapp, E.A. & Simpson, R.I. Statistical and mechanistic approaches to understanding the gas-phase fragmentation behavior of methionine sulfoxide containing peptides. J. Proteome Res. 3, 751-759 (2004).
10. Syka, J.E., Coon, J.J., Schroeder, M.J., Shabanowitz, J. & Hunt, D.F. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA 101, 9528-9533 (2004).
11. Breci, L.A., Tabb, D.L., Yates, J.R. III. & Wysocki, V.H. Cleavage N-terminal to proline: Analysis of a database of peptide tandem mass spectra. Anal. Chem. 75, 1963-1971 (2003).
12. Tabb, D.L. et al. Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal. Chem. 75, 1155-1163 (2003).
13. Paizs, B. & Suhai, S. Towards understanding some ion intensity relationships for the tandem mass spectra of protonated peptides. Rapid Commun. Mass Spectrom. 16, 1699-1702 (2002).
14. Tabb, D.L., Huang, Y., Wysocki, V.H. & Yates, J.R. III. Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 76, 1243-1248 (2004).
15. Ballard, K.D. & Gaskel, S.J. Dehydration of peptide [M+H]+ ions in the gas phase. J. Am. Soc. Mass Spectrom. 4, 477-481 (1993).
16. Hunt, D.F., Yates, J.R. III, Shabanowitz, J., Winston, S. & Hauer, C.R. Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 83, 6233-6237 (1986).
17. Jonscher, K.R. & Yates, J.R. III. The quadrupole ion trap mass spectrometer-a small solution to a big challenge. Anal. Biochem. 244, 1-15 (1997).
18. Chernushevich, I.V., Loboda, A.V. & Thomson, B.A. An introduction to quadrupole-time-of-flight mass spectrometry. J. Mass Spectrom. 36, 849-865 (2001).
19. Medzihradszky, K.F. et al. The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal. Chem. 72, 552-558 (2000).
20. Fenyo, D. & Beavis, R.C. A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 75, 768-774 (2003).
21. Craig, R. & Beavis, R.C. TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467 (2004).
22. Geer, L.Y. et al. Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964 (2004).
23. Link, A.J. et al. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17, 676-682 (1999).
24. Cargile, B.J., Bundy, J.L. & Stephenson, J.L. Jr. Potential for false positive identifications from large databases through tandem mass spectrometry. J. Proteome Res. 3, 1082-1085 (2004).
25. Higdon, R., Hogan, J.M., Van Belle, G. & Kolker, E. Randomized sequence databases for tandem mass spectrometry peptide and protein identification. OMICS 9, 364-379 (2005).
26. Keller, A., Nesvizhskii, A.I., Kolker, E. & Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392 (2002).
27. Chen, Y., Kwon, S.W., Kim, S.C. & Zhao, Y. Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra. J. Proteome Res. 4, 998-1005 (2005).
28. Gibbons, F.D., Elias, J.E., Gygi, S.P. & Roth, F.P. SILVER helps assign peptides to tandem mass spectra using intensity-based scoring. J. Am. Soc. Mass Spectrom. 15, 910-912 (2004).
29. Lilley, K.S. & Friedman, D.B. All about DIGE: Quantification technology for differential-display 2D-gel proteomics. Expert Rev. Proteomics 1, 401-409 (2004).
30. Tabb, D.L., Narasimhan, C., Strader, M.B. & Hettich, R.L. DBDigger: reorganized proteomic database identification that improves flexibility and speed. Anal. Chem. 77, 2464-2474 (2005).
31. Kapp, E.A. et al. Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal. Chem. 75, 6251-6264 (2003).
32. Geiger, T. & Clarke, S. Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides. Succinimide-linked reactions that contribute to protein degradation. J. Biol. Chem. 262, 785-794 (1987).
33. Tsaprailis, G. et al. A mechanistic investigation of the enhanced cleavage at histidine in the gas-phase dissociation of protonated peptides. Anal. Chem. 76, 2083-2094 (2004).
34. Bradshaw, R.A. Revised draft guidelines for proteomic data publication. Mol. Cell. Proteomics 4, 1223-1225 (2005).
35. Carr, S. et al. The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol. Cell. Proteomics 3, 531-533 (2004).
36. Yang, X. et al. DBParser: Web-based software for shotgun proteomic data analyses. J. Proteome Res. 3, 1002-1008 (2004).
37. Tabb, D.L., McDonald, W.H. & Yates, J.R. III. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1, 21-26 (2002).