Comment on "unbiased statistical analysis for multi-stage proteomic search strategies"

Journal of Proteome Research

Volumn 10, Issue 4, 2011, Pages 2123-2127

  Bern, Marshall ^a   Kil, Yong J ^a  

^a PALO ALTO RESEARCH CENTER   (United States)

Author keywords

bioinformatics; mass spectrometry; Paragon; peptide identification; proteomics; X!Tandem

Indexed keywords

ARTICLE; MATHEMATICAL ANALYSIS; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEOMICS; STATISTICAL ANALYSIS; TIME OF FLIGHT MASS SPECTROMETRY;

ALGORITHMS; DATABASES, PROTEIN; PROTEINS; PROTEOMICS; SEARCH ENGINE; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 79953711171     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr101143m     Document Type: Article

References (13)

1. Bern, M.; Goldberg, D. Improved ranking functions for protein and modification-site identifications J. Comp. Biol. 2008, 15, 705-719
2. Creasy, D. M.; Cottrell, J. S. Error tolerant searching of uninterpreted tandem mass spectrometry data Proteomics 2002, 2 (10) 1426-1434 (Pubitemid 35340023)
3. Nesvizhskii, A. I.; Roos, F. F.; Grossmann, J.; Vogelzang, M.; Eddes, J. S.; Gruissem, W.; Baginsky, S.; Aebersold, R. Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of posttranslational modifications, sequence polymorphisms, and novel peptides Mol. Cell. Proteomics 2006, 5 (4) 652-670
4. Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra Bioinformatics 2004, 20 (9) 1466-1467 (Pubitemid 38931421)
5. Shilov, I. V.; Seymour, S. L.; Patel, A. A.; Loboda, A.; Tang, W. H.; Keating, S. P.; Hunter, C. L.; Nuwaysir, L. M.; Schaeffer, D. A. The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra Mol. Cell. Proteomics 2007, 6, 1638-1655 (Pubitemid 47506173)
6. Everett, L. J.; Bierl, C.; Master, S. R. Unbiased statistical analysis for multi-stage proteomic search strategies J. Proteome Res. 2010, 9 (2) 700-707
7. 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 (Pubitemid 46358868)
8. Moore, R. E.; Young, M. K.; Lee, T. D. Qscore: an algorithm for evaluating SEQUEST database search results J. Am. Soc. Mass Spectrom. 2002, 13 (4) 378-386 (Pubitemid 34280088)
9. Bern, M.; Phinney, B. S.; Goldberg, D. Reanalysis of Tyrannosaurus rex mass spectra J. Proteome Res. 2009, 8 (9) 4328-4332
10. Craig, R.; Beavis, R. C. A method for reducing the time required to match protein sequences with tandem mass spectra Rapid Commun. Mass Spectrom. 2003, 17 (20) 2310-2316 (Pubitemid 37243315)
11. Bern, M.; Cai, Y.; Goldberg, D. Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry Anal. Chem. 2007, 79, 1393-1400
12. Falkner, J. A.; Kachman, M.; Veine, D. M.; Walker, A.; Strahler, J. R.; Andrews, P. C. Validated MALDI-TOF/TOF mass spectra for protein standards J. Am. Soc. Mass Spectrom. 2007, 18, 850-855 (Pubitemid 46617280)
13. Weatherly, D. B.; Atwood, J. A.; Minning, T. A.; Cavola, C; Tarleton, R. L.; Orlando, R. A heuristic method for assigning a false-discovery rate for protein identifications from Mascot database search results Mol. Cell. Proteomics 2005, 4 (6) 762-772 (Pubitemid 40873005)