Value of using multiple proteases for large-scale mass spectrometry-based proteomics

Journal of Proteome Research

Volumn 9, Issue 3, 2010, Pages 1323-1329

  Swaney, Danielle L ^a   Wenger, Craig D ^a   Coon, Joshua J ^a  

^a UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

Electron transfer dissociation; Mass spectrometry; Model organisms; Proteomics

Indexed keywords

PROTEINASE; TRYPSIN;

ALGORITHM; ARTICLE; DECISION TREE; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SACCHAROMYCES CEREVISIAE;

COMPUTER SIMULATION; MASS SPECTROMETRY; MODELS, BIOLOGICAL; PEPTIDE FRAGMENTS; PEPTIDE HYDROLASES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

SACCHAROMYCES CEREVISIAE;

EID: 77949786295     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr900863u     Document Type: Article

References (32)

1. Washburn, M. P.; Wolters, D.; Yates, J. R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19 (3), 242-247.
2. de Godoy, L. M. F.; Olsen, J. V.; Cox, J.; Nielsen, M. L.; Hubner, N. C.; Frohlich, F.; Walther, T. C.; Mann, M. Comprehensive massspectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455 (7217), 1251-1254.
3. de Godoy, L.; Olsen, J.; de Souza, G.; Li, G.; Mortensen, P.; Mann, M. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol. 2006, 7 (6), R50.
4. Peng, J. M.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J. Proteome Res. 2003, 2 (1), 43-50.
5. Dongre, A. R.; Jones, J. L.; Somogyi, A.; Wysocki, V. H. Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: Evidence for the mobile proton model. J. Am. Chem. Soc. 1996, 118 (35), 8365-8374.
6. Huang, Y. Y.; Triscari, J. M.; Tseng, G. C.; Pasa-Tolic, L.; Lipton, M. S.; Smith, R. D.; Wysocki, V. H. Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal. Chem. 2005, 77 (18), 5800-5813.
7. Good, D. M.; Wirtala, M.; McAlister, G. C.; Coon, J. J. Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry. Mol. Cell. Proteomics 2007, 6 (11), 1942-1951.
8. Swaney, D. L.; McAlister, G. C.; Coon, J. J. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat. Methods 2008, 5 (11), 959-964.
9. Aebersold, R. H.; Leavitt, J.; Saavedra, R. A.; Hood, L. E.; Kent, S. B. H. Internal amino-acid sequence-analysis of proteins separated by one-dimensional or two-dimensional gel-electrophoresis after insitu protease digestion on nitrocellulose. Proc. Natl. Acad. Sci. U.S.A. 1987, 84 (20), 6970-6974.
10. Harper, R. G.; Workman, S. R.; Schuetzner, S.; Timperman, A. T.; Sutton, J. N. In Low-molecular-weight human serum proteome using ultrafiltration, isoelectric focusing, and mass spectrometry; Wiley-V C H Verlag Gmbh: Weinheim, 2004; pp 1299-1306.
11. MacCoss, M. J.; McDonald, W. H.; Saraf, A.; Sadygov, R.; Clark, J. M.; Tasto, J. J.; Gould, K. L.; Wolters, D.; Washburn, M.; Weiss, A.; Clark, J. I.; Yates, J. R. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (12), 7900-7905.
12. Schlosser, A.; Vanselow, J. T.; Kramer, A. Mapping of Phosphorylation Sites by a Multi-Protease Approach with Specific Phosphopeptide Enrichment and NanoLC-MS/MS Analysis. Anal. Chem. 2005, 77 (16), 5243-5250.
13. Wang, B.; Malik, R.; Nigg, E. A.; KoÌr̂ner, R. Evaluation of the Low-Specificity Protease Elastase for Large-Scale Phosphoproteome Analysis. Anal. Chem. 2008, 80 (24), 9526-9533.
14. Biringer, R. G.; Amato, H.; Harrington, M. G.; Fonteh, A. N.; Riggins, J. N.; Huhmer, A. F. R. Enhanced sequence coverage of proteins in human cerebrospinal fluid using multiple enzymatic digestion and linear ion trap LC-MS/MS. Brief Funct. Genomic Proteomic 2006, 5 (2), 144-153.
15. Choudhary, G.; Wu, S.-L.; Shieh, P.; Hancock, W. S. Multiple Enzymatic Digestion for Enhanced Sequence Coverage of Proteins in Complex Proteomic Mixtures Using Capillary LC with Ion Trap MS/MS. J. Proteome Res. 2003, 2 (1), 59-67.
16. Elenitoba-Johnson, K. S. J.; Crockett, D. K.; Schumacher, J. A.; Jenson, S. D.; Coffin, C. M.; Rockwood, A. L.; Lim, M. S. Proteomic identification of oncogenic chromosomal translocation partners encoding chimeric anaplastic lymphoma kinase fusion proteins.Proc. Natl. Acad. Sci. U.S.A. 2006, 103 (19), 7402-7407.
17. Kapp, E. A.; Schutz, F.; Reid, G. E.; Eddes, J. S.; Moritz, R. L.; O'Hair, R. A. J.; Speed, T. P.; Simpson, R. J. Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal. Chem. 2003, 75 (22), 6251-6264.
18. Syka, J. E. P.; 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. U.S.A. 2004, 101 (26), 9528-9533.
19. Zubarev, R. A.; Kelleher, N. L.; McLafferty, F. W. Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc. 1998, 120 (13), 3265-3266.
20. Villen, J.; Beausoleil, S. A.; Gerber, S. A.; Gygi, S. P. Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (5), 1488-1493.
21. Ficarro, S. B.; Zhang, Y.; Lu, Y.; Moghimi, A. R.; Askenazi, M.; Hyatt, E.; Smith, E. D.; Boyer, L.; Schlaeger, T. M.; Luckey, C. J.; Marto, J. A. Improved Electrospray Ionization Efficiency Compensates for Diminished Chromatographic Resolution and Enables Proteomics Analysis of Tyrosine Signaling in Embryonic Stem Cells. Anal. Chem. 2009, 81 (9), 3440-3447.
22. McAlister, G. C.; Berggren, W. T.; Griep-Raming, J.; Horning, S.; Makarov, A.; Phanstiel, D.; Stafford, G.; Swaney, D. L.; Syka, J. E. P.; Zabrouskov, V.; Coon, J. J. A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. J. Proteome Res. 2008, 7 (8), 3127-3136.
23. McAlister, G. C.; Phanstiel, D.; Good, D. M.; Berggren, W. T.; Coon, J. J. Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Anal. Chem. 2007, 79 (10), 3525-3534.
24. Good, D. M.; Wenger, C. D.; McAlister, G. C.; Bai, D. L.; Hunt, D. F.; Coon, J. J. Post-Acquisition ETD Spectral Processing for Increased Peptide Identifications. J. Am. Soc. Mass Spectrom. 2009, 20 (8), 1435-1440.
25. 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), 207-214.
26. Geer, L. Y.; Markey, S. P.; Kowalak, J. A.; Wagner, L.; Xu, M.; Maynard, D. M.; Yang, X. Y.; Shi, W. Y.; Bryant, S. H. Open mass spectrometry search algorithm. J. Proteome Res. 2004, 3 (5), 958-964.
27. Nesvizhskii, A. I.; Aebersold, R. Interpretation of Shotgun Proteomic Data: The Protein Inference Problem. Mol. Cell. Proteomics 2005, 4 (10), 1419-1440.
28. Ham, B. M.; Yang, F.; Jayachandran, H.; Jaitly, N.; Monroe, M. E.; Gritsenko, M. A.; Livesay, E. A.; Zhao, R.; Purvine, S. O.; Orton, D.; Adkins, J. N.; Camp, D. G.; Rossie, S.; Smith, R. D. The Influence of Sample Preparation and Replicate Analyses on HeLa Cell Phosphoproteome Coverage. J. Proteome Res. 2008, 7 (6), 2215-2221.
29. Ghaemmaghami, S.; Huh, W.-K.; Bower, K.; Howson, R. W.; Belle, A.; Dephoure, N.; O'Shea, E. K.; Weissman, J. S. Global analysis of protein expression in yeast. Nature 2003, 425 (6959), 737-741.
30. Huh, W.-K.; Falvo, J. V.; Gerke, L. C.; Carroll, A. S.; Howson, R. W.; Weissman, J. S.; O'Shea, E. K. Global analysis of protein localization in budding yeast. Nature 2003, 425 (6959), 686-691.
31. Gauci, S.; Helbig, A. O.; Slijper, M.; Krijgsveld, J.; Heck, A. J. R.; Mohammed, S. Lys-N and Trypsin Cover Complementary Parts of the Phosphoproteome in a Refined SCX-Based Approach. Anal. Chem. 2009, 81 (11), 4493-4501.
32. Molina, H.; Horn, D. M.; Tang, N.; Mathivanan, S.; Pandey, A. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (7), 2199-2204.