SQID: An intensity-incorporated protein identification algorithm for tandem mass spectrometry

Journal of Proteome Research

Volumn 10, Issue 4, 2011, Pages 1593-1602

  Li, Wenzhou ^a   Ji, Li ^a   Goya, Jonathan ^a   Tan, Guanhong ^a   Wysocki, Vicki H ^a  

^a University of Arizona   (United States)

Author keywords

database search; intensity; protein identification algorithm; tandem mass spectrometry

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SEQUENCE IDENTIFICATION; STATISTICAL ANALYSIS; TANDEM MASS SPECTROMETRY;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; CHROMATOGRAPHY, LIQUID; DROSOPHILA PROTEINS; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEOMICS; SACCHAROMYCES CEREVISIAE PROTEINS; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 79953676624     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr100959y     Document Type: Article

References (24)

1. Eng, J. K.; McCormack, A. L.; Yates, J. R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Soc. Mass Spectrom. 1994, 5 (11) 976-989
2. Craig, R.; Beavis, R. C. Tandem: matching proteins with mass spectra Bioinformatics 2004, 20 (9) 1466-1467 (Pubitemid 38931421)
3. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20 (18) 3551-3567 (Pubitemid 30007252)
4. Sadygov, R. G.; Cociorva, D.; Yates, J. R. Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book Nat. Methods 2004, 1 (13) 195-202
5. Wysocki, V. H.; Tsaprailis, G.; Smith, L. L; Breci, L. A. Mobile and localized protons: a framework for understanding peptide dissociation J. Mass Spectrom. 2000, 35 (12) 1399-1406 (Pubitemid 32063646)
6. Huang, 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 (Pubitemid 41324278)
7. Huang, Y.; Tseng, G. C.; Yuan, S.; Pasa-Tolic, L.; Lipton, M. S.; Smith, R. D.; Wysocki, V. H. A data-mining scheme for identifying peptide structural motifs responsible for different MS/MS fragmentation intensity patterns J. Proteome Res. 2008, 7 (1) 70-79 (Pubitemid 351171117)
8. Paizs, B.; Suhai, S. Fragmentation pathways of protonated peptides Mass Spectrom. Rev. 2005, 24 (4) 508-548
9. Zhang, Z. Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges Anal. Chem. 2004, 76 (14) 3908-3922 (Pubitemid 38943659)
10. Gibbons, F. D.; Elias, J. E.; Gygi, S. P.; Roth, F. P. SILVER helps assign peptides to tandem mass spectra using intensity-based scoring J. Am. Soc. Mass Spectrom. 2004, 15 (6) 910-912 (Pubitemid 38624240)
11. Havilio, M.; Haddad, Y.; Smilansky, Z. Intensity-based statistical scorer for tandem mass spectrometry Anal. Chem. 2003, 75 (3) 435-444 (Pubitemid 36176713)
12. Zhang, Z. Prediction of low-energy collision-induced dissociation spectra of peptides Anal. Chem. 2004, 76 (14) 3908-3922 (Pubitemid 38943659)
13. Elias, J. E.; Gibbons, F. D.; King, O. D.; Roth, F. P.; Gygi, S. P. Intensity-based protein identification by machine learning from a library of tandem mass spectra Nat. Biotechnol. 2004, 22 (2) 214-219 (Pubitemid 38160538)
14. Narasimhan, C.; Tabb, D. L; Verberkmoes, N. C.; Thompson, M. R.; Hettich, R. L.; Uberbacher, E. C. MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence Anal. Chem. 2005, 77 (23) 7581-7593 (Pubitemid 41746225)
15. Sun, S.; Meyer-Arendt, K.; Eichelberger, B. Improved validation of peptide MS/MS assignments using spectral intensity prediction Mol. Cell. Proteomics 2007, 6 (1) 1-17 (Pubitemid 46152687)
16. Zhou, C.; Bowler, L. D.; Feng, J. A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data BMC Bioinform. 2008, 9, 325
17. Stein, S. E.; Pudnick, P. A. NIST Peptide Tandem Mass Spectral Libraries. Yeast Peptide Mass Spectral Reference Data, Yeast, ion trap, Official Build Date: May. 14, 2009. Drosophila Peptide Mass Spectral Reference Data, Drosophila, ion trap, Official Build Date: July. 14, 2008. National Institute of Standards and Technology, Gaithersburg, MD, 20899. Downloaded from http://peptide.nist.gov on April 1, 2010.
18. Searle, B. C. Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies Proteomics 2010, 10 (6) 1265-1269
19. Lipton, M. S.; Pasa-Tolic, L.; Anderson, G. A.; Anderson, D. J.; Auberry, D. L.; Battista, J. R.; Daly, M. J.; Fredrickson, J.; Hixson, K. K.; Kostandarithes, H.; Masselon, C.; Markillie, L. M.; Moore, R. J.; Romine, M. F.; Shen, Y.; Stritmatter, E.; Tolic, N.; Udseth, H. R.; Venkateswaran, A.; Wong, K.; Zhao, R.; Smith, R. D. Globalanalysis of the Deinococ cus radiodurans proteome by using accurate mass tags Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (17) 11049-11054 (Pubitemid 34920877)
20. Kolker, E.; Picone, A. F.; Galperin, M. Y.; Romine, M. F.; Higdon, R.; Makarova, K. S.; Kolker, N.; Anderson, G. A.; Qiu, X.; Auberry, K. J.; Babnigg, G.; Beliaev, A. S.; Edlefsen, P.; Elias, D. A.; Gorby, Y. A.; Holzman, T.; Klappenbach, J. A.; Konstantinidis, K. T.; Land, M. L.; Lipton, M. S.; McCue, L.; Monroe, M.; Pasa-Tolic, L.; Pinchuk, G.; Purvine, S.; Serres, M. H.; Tsapin, S.; Zakrajsek, B. A.; Zhu, W.; Zhou, J.; Larimer, F. W.; Lawrence, C. E.; Riley, M.; Collart, F. R.; Yates, J. R.; Smith, R. D.; Giometti, C. S.; Nealson, K. H.; Fredrickson, J. K.; Tiedje, J. M. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (6) 2099-2104 (Pubitemid 40262018)
21. Keller, A.; Purvine, S.; Nesvizhskii, A. I.; Stolyar, S.; Goodlett, D. R.; Kolker, E. Experimental protein mixture for validating tandem mass spectral analysis OMICS 2002, 6 (2) 207-212 (Pubitemid 35278428)
22. Zhang, B.; Chambers, M. C.; Tabb, D. L. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency J. Proteome Res. 2007, 6 (9) 3549-3557 (Pubitemid 47522746)
23. Tabb, D. L.; Fernando, C. G.; Chambers, M. C. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis J. Proteome Res. 2007, 6 (2) 654-661 (Pubitemid 46340169)
24. Storey, J. D.; Tibshirani, R. Statistical significance for genome-wide studies Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (16) 9440-9445