Expanding tandem mass spectral libraries of phosphorylated peptides: Advances and applications

Journal of Proteome Research

Volumn 12, Issue 12, 2013, Pages 5971-5977

  Hu, Yingwei ^a   Lam, Henry ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

collision induced dissociation (CID); phosphoproteomics; tandem mass spectral libraries

Indexed keywords

PEPTIDE DERIVATIVE; PEPTIDE LIBRARY; PHOSPHOPEPTIDE;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CAENORHABDITIS ELEGANS; COLLISIONALLY ACTIVATED DISSOCIATION; COMPUTER PROGRAM; DROSOPHILA MELANOGASTER; EVALUATION; HUMAN; MUS MUSCULUS; NONHUMAN; PEPTIDE LIBRARY; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN DOMAIN; PROTEIN PHOSPHORYLATION; PROTEOMICS; REPRODUCIBILITY; SACCHAROMYCES CEREVISIAE; SEQUENCE DATABASE; TANDEM MASS SPECTROMETRY; ANIMAL; CHEMISTRY; METABOLISM; MOUSE; STANDARDS; STATISTICS AND NUMERICAL DATA; TUMOR CELL LINE;

ANIMALS; CAENORHABDITIS ELEGANS; CELL LINE, TUMOR; DROSOPHILA MELANOGASTER; HUMANS; MICE; PEPTIDE LIBRARY; PHOSPHOPEPTIDES; SACCHAROMYCES CEREVISIAE; TANDEM MASS SPECTROMETRY;

EID: 84890111730     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr4007443     Document Type: Article

References (44)

1. Khoury, G. A.; Baliban, R. C.; Floudas, C. A. Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database Sci. Rep. 2011, 1, 90
2. Derouiche, A.; Cousin, C.; Mijakovic, I. Protein phosphorylation from the perspective of systems biology Curr. Opin. Biotechnol. 2012, 23 (4) 585-590
3. Engholm-Keller, K.; Larsen, M. R. Technologies and challenges in large-scale phosphoproteomics Proteomics 2013, 13 (6) 910-31
4. Beausoleil, S. A.; Villen, J.; Gerber, S. A.; Rush, J.; Gygi, S. P. A probability-based approach for high-throughput protein phosphorylation analysis and site localization Nat. Biotechnol. 2006, 24 (10) 1285-1292
5. Lu, B.; Ruse, C.; Xu, T.; Park, S. K.; Yates, J. Automatic validation of phosphopeptide identifications from tandem mass spectra Anal. Chem. 2007, 79 (4) 1301-1310
6. Bodenmiller, B.; Campbell, D.; Gerrits, B.; Lam, H.; Jovanovic, M.; Picotti, P.; Schlapbach, R.; Aebersold, R. PhosphoPep - a database of protein phosphorylation sites in model organisms Nat. Biotechnol. 2008, 26 (12) 1339-1340
7. Eng, J. K.; Searle, B. C.; Clauser, K. R.; Tabb, D. L. A face in the crowd: recognizing peptides through database search Mol. Cell. Proteomics 2011, 10 (11) R111 009522
8. 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 1994, 5 (11) 976-989
9. Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20 (18) 3551-3567
10. Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra Bioinformatics 2004, 20 (9) 1466-7
11. Geer, L. Y.; Markey, S. P.; Kowalak, J. A.; Wagner, L.; Xu, M.; Maynard, D. M.; Yang, X.; Shi, W.; Bryant, S. H. Open mass spectrometry search algorithm J. Proteome Res. 2004, 3 (5) 958-964
12. Kim, S.; Mischerikow, N.; Bandeira, N.; Navarro, J. D.; Wich, L.; Mohammed, S.; Heck, A. J. R.; Pevzner, P. A. The generating function of CID, ETD and CID/ETD pairs of tandem mass spectra: Applications to database search Mol. Cell. Proteomics 2010, 9 (12) 2840-2852
13. Boersema, P. J.; Mohammed, S.; Heck, A. J. R. Phosphopeptide fragmentation and analysis by mass spectrometry J. Mass Spectrom. 2009, 44 (6) 861-878
14. Craig, R.; Cortens, J. C.; Fenyo, D.; Beavis, R. C. Using annotated peptide mass spectrum libraries for protein identification J. Proteome Res. 2006, 5 (8) 1843-1849
15. Frewen, B. E.; Merrihew, G. E.; Wu, C. C.; Noble, W. S.; MacCoss, M. J. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries Anal. Chem. 2006, 78 (16) 5678-84
16. Lam, H.; Deutsch, E. W.; Eddes, J. S.; Eng, J. K.; King, N.; Stein, S. E.; Aebersold, R. Development and validation of a spectral library searching method for peptide identification from MS/MS Proteomics 2007, 7 (5) 655-667
17. Dasari, S.; Chambers, M. C.; Martinez, M. A.; Carpenter, K. L.; Ham, A. J.; Vega-Montoto, L. J.; Tabb, D. L. Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment J. Proteome Res. 2012, 11 (3) 1686-95
18. Zhang, X.; Li, Y.; Shao, W.; Lam, H. Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis Proteomics 2011, 11 (6) 1075-85
19. Lam, H. Building and searching tandem mass spectral libraries for peptide identification Mol. Cell. Proteomics 2011, 10 (12) R111-008565
20. Marx, H.; Lemeer, S.; Schliep, J. E.; Matheron, L.; Mohammed, S.; Cox, J.; Mann, M.; Heck, A. J. R.; Kuster, B. A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics Nat. Biotechnol. 2013, 31 (6) 557-564
21. Palumbo, A. M.; Smith, S. A.; Kalcic, C. L.; Dantus, M.; Stemmer, P. M.; Reid, G. E. Tandem mass spectrometry strategies for phosphoproteome analysis Mass Spectrom. Rev. 2011, 30 (4) 600-625
22. Rikova, K.; Guo, A.; Zeng, Q.; Possemato, A.; Yu, J.; Haack, H.; Nardone, J.; Lee, K.; Reeves, C.; Li, Y.; Hu, Y.; Tan, Z.; Stokes, M.; Sullivan, L.; Mitchell, J.; Wetzel, R.; MacNeill, J.; Ren, J. M.; Yuan, J.; Bakalarski, C. E.; Villen, J.; Kornhauser, J. M.; Smith, B.; Li, D.; Zhou, X.; Gygi, S. P.; Gu, T.-L.; Polakiewicz, R. D.; Rush, J.; Comb, M. J. Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer Cell 2007, 131 (6) 1190-1203
23. Beausoleil, S. A.; Jedrychowski, M.; Schwartz, D.; Elias, J. E.; Villen, J.; Li, J.; Cohn, M. A.; Cantley, L. C.; Gygi, S. P. Large-scale characterization of HeLa cell nuclear phosphoproteins Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (33) 12130-5
24. Li, X.; Gerber, S. A.; Rudner, A. D.; Beausoleil, S. A.; Haas, W.; Villén, J.; Elias, J. E.; Gygi, S. P. Large-scale phosphorylation analysis of α-factor-arrested Saccharomyces cerevisiae J. Proteome Res. 2007, 6 (3) 1190-1197
25. Hu, Y.; Li, Y.; Lam, H. A semi-empirical approach for predicting unobserved peptide MS/MS spectra from spectral libraries Proteomics 2011, 11 (24) 4702-11
26. Deutsch, E. W.; Lam, H.; Aebersold, R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows EMBO Rep. 2008, 9 (5) 429-34
27. Franz-Wachtel, M.; Eisler, S. A.; Krug, K.; Wahl, S.; Carpy, A.; Nordheim, A.; Pfizenmaier, K.; Hausser, A.; Macek, B. Global detection of protein kinase D-dependent phosphorylation events in nocodazole-treated human cells Mol. Cell. Proteomics 2012, 11 (5) 160-70
28. Rudnick, P. A.;; Clauser, K. R.;; Lane, W. S.;; Martens, L.;; McDonald, W. H.;; Meyer-Arendt, K.;; Searle, B. C.;; Kowalak, J. A. iPRG: Informatic Evaluation of Phosphopeptide Identification and Phosphosite Localization. Association of Biomolecular Resource Facilities (ABRF) Annual Meeting, Sacramento, CA, 2010.
29. Huttlin, E. L.; Jedrychowski, M. P.; Elias, J. E.; Goswami, T.; Rad, R.; Beausoleil, S. A.; Villen, J.; Haas, W.; Sowa, M. E.; Gygi, S. P. A tissue-specific atlas of mouse protein phosphorylation and expression Cell 2010, 143 (7) 1174-89
30. MacLean, B.; Eng, J. K.; Beavis, R. C.; McIntosh, M. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine Bioinformatics 2006, 22 (22) 2830-2832
31. Keller, A.; Eng, J.; Zhang, N.; Li, X.-j.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats Mol. Syst. Biol. 2005, 1, 2005-0017
32. Deutsch, E. W.; Mendoza, L.; Shteynberg, D.; Farrah, T.; Lam, H.; Tasman, N.; Sun, Z.; Nilsson, E.; Pratt, B.; Prazen, B.; Eng, J. K.; Martin, D. B.; Nesvizhskii, A. I.; Aebersold, R. A guided tour of the Trans-Proteomic Pipeline Proteomics 2010, 10 (6) 1150-9
33. UniProt Consortium, Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 2013, 41, (D1), D43-D47.
34. Elias, J. E.; Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat. Methods 2007, 4 (3) 207-14
35. 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. 2002, 74 (20) 5383-5392
36. Choi, H.; Ghosh, D.; Nesvizhskii, A. I. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling J. Proteome Res. 2008, 7 (1) 286-92
37. Shteynberg, D.; Deutsch, E. W.; Lam, H.; Eng, J. K.; Sun, Z.; Tasman, N.; Mendoza, L.; Moritz, R. L.; Aebersold, R.; Nesvizhskii, A. I. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates Mol. Cell. Proteomics 2011, 10 (12) M111-007690
38. Taus, T.; Köcher, T.; Pichler, P.; Paschke, C.; Schmidt, A.; Henrich, C.; Mechtler, K. Universal and confident phosphorylation site localization using phosphoRS J. Proteome Res. 2011, 10 (12) 5354-5362
39. Shteynberg, D. D. E.; Mendoza, L.; Slagel, J.; Lam, H.; Nesvizhskii, A.; Moritz, R. PTMProphet: TPP Software for Validation of Modified Site Locations on Post-Translationally Modified Peptides. 60th American Society for Mass Spectrometry (ASMS) Annual Conference, Vancouver, Canada, 2012.
40. Lam, H.; Deutsch, E. W.; Eddes, J. S.; Eng, J. K.; Stein, S. E.; Aebersold, R. Building consensus spectral libraries for peptide identification in proteomics Nat. Methods 2008, 5 (10) 873-5
41. Lam, H.; Deutsch, E. W.; Aebersold, R. Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics J. Proteome Res. 2010, 9 (1) 605-10
42. Christensen, G. L.; Kelstrup, C. D.; Lyngso, C.; Sarwar, U.; Bogebo, R.; Sheikh, S. P.; Gammeltoft, S.; Olsen, J. V.; Hansen, J. L. Quantitative phosphoproteomics dissection of seven-transmembrane receptor signaling using full and biased agonists Mol. Cell. Proteomics 2010, 9 (7) 1540-53
43. Blasius, M.; Forment, J. V.; Thakkar, N.; Wagner, S. A.; Choudhary, C.; Jackson, S. P. A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1 Genome Biol. 2011, 12 (8) R78
44. Ahrne, E.; Masselot, A.; Binz, P. A.; Muller, M.; Lisacek, F. A simple workflow to increase MS2 identification rate by subsequent spectral library search Proteomics 2009, 9 (6) 1731-6