The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics

Analytical and Bioanalytical Chemistry

Volumn 389, Issue 5, 2007, Pages 1409-1419

  Bakalarski, Corey E ^a   Haas, Wilhelm ^a   Dephoure, Noah E ^a   Gygi, Steven P ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Database searching; High throughput proteomics; Mass accuracy; Phosphorylation analysis; Shotgun sequencing

Indexed keywords

ALGORITHMS; CYCLOTRON RESONANCE; DATA REDUCTION; DATABASE SYSTEMS; FOURIER TRANSFORMS; MASS SPECTROMETRY; PHOSPHORYLATION;

DATABASE SEARCHING; HIGH-THROUGHPUT PROTEOMICS; MASS ACCURACY; PHOSPHORYLATION ANALYSIS; SHOTGUN SEQUENCING;

AMINO ACIDS;

PEPTIDE; PHOSPHOPROTEIN;

ALGORITHM; ARTICLE; INSTRUMENTATION; METHODOLOGY; MOLECULAR WEIGHT; PROTEOMICS; TANDEM MASS SPECTROMETRY;

ALGORITHMS; MOLECULAR WEIGHT; PEPTIDES; PHOSPHOPROTEINS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 35648969575     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-007-1563-x     Document Type: Article

References (24)

1. Syka JE, Marto JA, Bai DL, Horning S, Senko MW, Schwartz JC, Ueberheide B, Garcia B, Busby S, Muratore T, Shabanowitz J, Hunt DF (2004) J Proteome Res 3:621-626
2. Florens L, Washburn MP, Raine JD, Anthony RM, Grainger M, Haynes JD, Moch JK, Muster N, Sacci JB, Tabb DL, Witney AA, Wolters D, Wu Y, Gardner MJ, Holder AA, Sinden RE, Yates JR, Carucci DJ (2002) Nature 419:520-526
3. Everley PA, Bakalarski CE, Elias JE, Waghorne CG, Beausoleil SA, Gerber SA, Faherty BK, Zetter BR, Gygi SP (2006) J Proteome Res 5:1224-1231
4. Lasonder E, Ishihama Y, Andersen JS, Vermunt AM, Pain A, Sauerwein RW, Eling WM, Hall N, Waters AP, Stunnenberg HG, Mann M (2002) Nature 419:537-542
5. Dieguez-Acuna FJ, Gerber SA, Kodama S, Elias JE, Beausoleil SA, Faustman D, Gygi SP (2005) Mol Cell Proteomics 4:1459-1470
6. Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP (2004) Proc Natl Acad Sci USA 101:12130-12135
7. Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP (2006) Nat Biotechnol 24:1285-1292
8. Villen J, Beausoleil SA, Gerber SA, Gygi SP (2007) Proc Natl Acad Sci USA 104:1488-1493
9. Li X, Gerber SA, Rudner AD, Beausoleil SA, Haas W, Villen J, Elias JE, Gygi SP (2007) J Proteome Res 6:1190-1197
10. Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M (2006) Cell 127:635-648
11. Olsen JV, Ong SE, Mann M (2004) Mol Cell Proteomics 3:608-614
12. Mayya V, Rezaul K, Cong YS, Han D (2005) Mol Cell Proteomics 4:214-223
13. Haas W, Faherty BK, Gerber SA, Elias JE, Beausoleil SA, Bakalarski CE, Li X, Villen J, Gygi SP (2006) Mol Cell Proteomics 5:1326-1337
14. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Electrophoresis 20:3551-3567
15. Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH (2004) J Proteome Res 3:958-964
16. Eng JK, McCormack AL, Yates I, John R (1994) J Am Soc Mass Spectrom 5:976-989
17. Craig R, Beavis RC (2004) Bioinformatics 20:1466-1467
18. Guthrie C, Fink GR (1991) Guide to yeast genetics and molecular biology. Academic, San Diego
19. Mortimer RK, Johnston JR (1986) Genetics 113:35-43
20. Shevchenko A, Wilm M, Vorm O, Mann M (1996) Anal Chem 68:850-858
21. Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R (2004) Nat Biotechnol 22:1459-1466
22. Elias JE, Gygi SP (2007) Nat Methods 4:207-214
23. Elias JE, Haas W, Faherty BK, Gygi SP (2005) Nat Methods 2:667-675
24. Liu H, Sadygov RG, Yates JR 3rd (2004) Anal Chem 76:4193-4201