Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics

Molecular and Cellular Proteomics

Volumn 13, Issue 8, 2014, Pages 2056-2071

  Toprak, Umut H ^a,c,d   Gillet, Ludovic C ^a   Maiolica, Alessio ^a   Navarro, Pedro ^a,e   Leitner, Alexander ^a   Aebersold, Ruedi ^a,b  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c UNIVERSITY OF GENEVA   (Switzerland)

^d EPFL   (Switzerland)

^e JOHANNES GUTENBERG UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE FRAGMENT; PEPTIDE;

ALGORITHM; ARTICLE; HUMAN; MASS SPECTROMETER; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PHOSPHORYLATION; PROTEOMICS; TANDEM MASS SPECTROMETRY; COMPUTER PROGRAM; ISOLATION AND PURIFICATION; PROCEDURES;

ALGORITHMS; MASS SPECTROMETRY; PEPTIDES; PROTEOMICS; SOFTWARE;

EID: 84904094826     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O113.036475     Document Type: Article

References (45)

1. Paizs, B., and Suhai, S. (2005) Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 24, 508-548
2. Steen, H., and Mann, M. (2004) The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Bio. 5, 699-711 (Pubitemid 39208180)
3. Nesvizhskii, A. (2007) Protein Identification by Tandem Mass Spectrometry and Sequence Database Searching. In: Matthiesen, R., ed. Mass Spectrometry Data Analysis in Proteomics, pp. 87-119, Humana Press
4. Zhang, Z. (2004) Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 76, 3908-3922
5. Zhang, Z. (2005) Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal. Chem. 77, 6364-6373
6. Zhang, Z. (2011) Prediction of collision-induced-dissociation spectra of peptides with post-translational or process-induced modifications. Anal. Chem. 83, 8642-8651
7. Li, W., Ji, L., Goya, J., Tan, G., and Wysocki, V. H. (2011) SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometry. J. Proteome Res. 10, 1593-1602
8. Craig, R., Cortens, J. P., and Beavis, R. C. (2005) The use of proteotypic peptide libraries for protein identification. Rapid Commun. Mass Sp.: RCM 19, 1844-1850 (Pubitemid 40886710)
9. Desiere, F., Deutsch, E. W., King, N. L., Nesvizhskii, A. I., Mallick, P., Eng, J., Chen, S., Eddes, J., Loevenich, S. N., and Aebersold, R. (2006) The PeptideAtlas project. Nucleic Acids Res. 34, D655-D658
10. Jones, P., Cote, R. G., Martens, L., Quinn, A. F., Taylor, C. F., Derache, W., Hermjakob, H., and Apweiler, R. (2006) PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 34, D659-D663
11. de Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Frohlich, F., Walther, T. C., and Mann, M. (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254
12. Riffle, M., and Eng, J. K. (2009) Proteomics data repositories. Proteomics 9, 4653-4663
13. Fenyo, D., Eriksson, J., and Beavis, R. (2010) Mass spectrometric protein identification using the global proteome machine. Methods Mol. Biol. 673, 189-202
14. Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J., and Mann, M. (2011) Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation. Mol. Cell. Proteomics 10
15. Vizcaino, J. A., Cote, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., O'Kelly, G., Schoenegger, A., Ovelleiro, D., Perez-Riverol, Y., Reisinger, F., Rios, D., Wang, R., and Hermjakob, H. (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41, D1063-D1069
16. Farrah, T., Deutsch, E. W., Hoopmann, M. R., Hallows, J. L., Sun, Z., Huang, C. Y., and Moritz, R. L. (2013) The state of the human proteome in 2012 as viewed through PeptideAtlas. J. Proteome Res. 12, 162-171
17. Domon, B., and Aebersold, R. (2010) Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 28, 710-721
18. Stein, S. E., and Scott, D. R. (1994) Optimization and Testing of Mass-Spectral Library Search Algorithms for Compound Identification. J. Am. Soc. Mass Spectr. 5, 859-866
19. Beer, I., Barnea, E., Ziv, T., and Admon, A. (2004) Improving large-scale proteomics by clustering of mass spectrometry data. Proteomics 4, 950-960 (Pubitemid 38445955)
20. Frewen, B. E., Merrihew, G. E., Wu, C. C., Noble, W. S., and MacCoss, M. J. (2006) Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem. 78, 5678-5684 (Pubitemid 44265027)
21. Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K., King, N., Stein, S. E., and Aebersold, R. (2007) Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7, 655-667 (Pubitemid 46453760)
22. Sherwood, C. A., Eastham, A., Lee, L. W., Risler, J., Vitek, O., and Martin, D. B. (2009) Correlation between y-Type Ions Observed in Ion Trap and Triple Quadrupole Mass Spectrometers. J. Proteome Res. 8, 4243-4251
23. MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., Kern, R., Tabb, D. L., Liebler, D. C., and MacCoss, M. J. (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966-968
24. Yen, C. Y., Houel, S., Ahn, N. G., and Old, W. M. (2011) Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library. Mol. Cell. Proteomics 10
25. Wan, K. X., Vidavsky, I., and Gross, M. L. (2002) Comparing similar spectra: from similarity index to spectral contrast angle. J. Am. Soc. Mass Spectr. 13, 85-88 (Pubitemid 34552627)
26. Tabb, D. L., MacCoss, M. J., Wu, C. C., Anderson, S. D., and Yates, J. R. (2003) Similarity among tandem mass spectra from proteomic experiments: Detection, significance, and utility. Anal. Chem. 75, 2470-2477 (Pubitemid 36582834)
27. Wang, J. A., Perez-Santiago, J., Katz, J. E., Mallick, P., and Bandeira, N. (2010) Peptide Identification from Mixture Tandem Mass Spectra. Mol. Cell. Proteomics 9, 1476-1485
28. Yates, J. R., 3rd, Morgan, S. F., Gatlin, C. L., Griffin, P. R., and Eng, J. K. (1998) Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis. Anal. Chem. 70, 3557-3565
29. Liu, J., Bell, A. W., Bergeron, J. J. M., Yanofsky, C. M., Carrillo, B., Beaudrie, C. E. H., and Kearney, R. E. (2007) Methods for peptide identification by spectral comparison. Proteome Sci. 5, 3
30. de Graaf, E. L., Altelaar, A. F., van Breukelen, B., Mohammed, S., and Heck, A. J. (2011) Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra. J. Proteome Res. 10, 4334-4341
31. Reiter, L., Rinner, O., Picotti, P., Huttenhain, R., Beck, M., Brusniak, M. Y., Hengartner, M. O., and Aebersold, R. (2011) mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods 8, 430-435
32. Wolski, W. E., Lalowski, M., Martus, P., Herwig, R., Giavalisco, P., Gobom, J., Sickmann, A., Lehrach, H., and Reinert, K. (2005) Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC bioinformatics 6, 285
33. Gillet, L. C., Navarro, P., Tate, S., Rost, H., Selevsek, N., Reiter, L., Bonner, R., and Aebersold, R. (2012) Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics: MCP 11, O111 016717
34. Bodenmiller, B., and Aebersold, R. (2010) Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics. Method Enzymol. 470, 317-334
35. Chambers, M. C., Maclean, B., Burke, R., Amodei, D., Ruderman, D. L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T. A., Brusniak, M. Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S. L., Nuwaysir, L. M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E. W., Moritz, R. L., Katz, J. E., Agus, D. B., MacCoss, M., Tabb, D. L., and Mallick, P. (2012) A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918-920
36. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search. Anal. Chem. 74, 5383-5392 (Pubitemid 35215372)
37. Kyte, J., and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132
38. Wells, J. M., and McLuckey, S. A. (2005) Collision-induced dissociation (CID) of peptides and proteins. Method Enzymol. 402, 148-185
39. Lau, K. W., Hart, S. R., Lynch, J. A., Wong, S. C., Hubbard, S. J., and Gaskell, S. J. (2009) Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides. Rapid Commun. Mass Sp.: RCM 23, 1508-1514
40. Second, T. P., Blethrow, J. D., Schwartz, J. C., Merrihew, G. E., MacCoss, M. J., Swaney, D. L., Russell, J. D., Coon, J. J., and Zabrouskov, V. (2009) Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal. Chem. 81, 7757-7765
41. Zubarev, R. A., and Makarov, A. (2013) Orbitrap mass spectrometry. Anal. Chem. 85, 5288-5296
42. Deutsch, E. W., Lam, H., and Aebersold, R. (2008) PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. Embo. Rep. 9, 429-434 (Pubitemid 351627279)
43. Picotti, P., Rinner, O., Stallmach, R., Dautel, F., Farrah, T., Domon, B., Wenschuh, H., and Aebersold, R. (2010) High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Methods 7, 43-46
44. Marx, H., Lemeer, S., Schliep, J. E., Matheron, L., Mohammed, S., Cox, J., Mann, M., Heck, A. J., and Kuster, B. (2013) A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics. Nat. Biotechnol. 31, 557-564
45. Boersema, P. J., Mohammed, S., and Heck, A. J. (2009) Phosphopeptide fragmentation and analysis by mass spectrometry. J. Mass Spectrom. 44, 861-878