Spectral library generating function for assessing spectrum-spectrum match significance

Journal of Proteome Research

Volumn 12, Issue 9, 2013, Pages 3944-3951

  Wang, Mingxun ^a,b   Bandeira, Nuno ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

algorithm; bioinformatics; Generating Function; p value; proteomics; Spectral Libraries; statistics; Tandem Mass Spectrometry

Indexed keywords

PEPTIDE FRAGMENT;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; DEAMINATION; LIBRARY; NULL HYPOTHESIS; PEPTIDE LIBRARY; PRIORITY JOURNAL; PROBABILITY; PROTEOMICS; SPECTRUM; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; TANDEM MASS SPECTROMETRY;

DATA INTERPRETATION, STATISTICAL; DATABASES, PROTEIN; FUNGAL PROTEINS; HELA CELLS; HUMANS; PEPTIDE FRAGMENTS; PEPTIDE MAPPING; PROTEOME; SEARCH ENGINE; SENSITIVITY AND SPECIFICITY; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 84883749843     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400230p     Document Type: Article

References (23)

1. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics Nature 2003, 422, 198-207
2. Eng, J.; AL., M.; Yates, J. 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, 976-989
3. Creasy, D.; Cottrell, J. Error tolerant searching of uninterpreted tandem mass spectrometry data Proteomics 2002, 2, 1426-1434
4. Kim, S.; Mischerikow, N.; Bandeira, N.; Navarro, J. D.; Wich, L.; Mohammed, S.; Heck, A. J.; Pevzner, P. A. The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: Applications to database search Mol. Cell. Proteomics 2010, 9, 2840-2852
5. Yates, J. R.; Morgan, S. F.; Gatlin, C. L.; Griffin, P. R.; Eng, J. K. Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis Anal. Chem. 1998, 70, 3557-3565
6. Stein, S. An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data J. Am. Soc. Mass Spectrom. 1999, 10, 770-781
7. Craig, R.; Cortens, J. C.; Fenyo, D.; Beavis, R. C. Using annotated peptide mass spectrum libraries for protein identification J. Proteome Res. 2006, 5, 1843-1849
8. Frewen, B. E.; Merrihew, G. E.; Wu, C. C.; Noble, W. S.; MacCoss, M. J. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries Anal. Chem. 2006, 78, 5678-5684
9. Lam, H.; Deutsch, E. W.; Eddes, J. S.; Eng, J. K.; King, N.; Stein, S. E.; Aebersold, R. Development and validation of a spectral library searching method for peptide identification from MS/MS Proteomics 2007, 7, 655-667
10. Wang, J.; Pérez-Santiago, J.; Katz, J. E.; Mallick, P.; Bandeira, N. Peptide identification from mixture tandem mass spectra Mol. Cell. Proteomics 2010, 9, 1476-1485
11. Yen, C. Y.; Houel, S.; Ahn, N. G.; Old, W. M. Spectrum-to-spectrum searching using a proteome-wide spectral library Mol. Cell. Proteomics 2011, 10.1074/mcp.M111.007666
12. Dasari, S.; Chambers, M. C.; Martinez, M. A.; Carpenter, K. L.; Ham, A. J.; Vega-Montoto, L. J.; Tabb, D. L. Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment J. Proteome Res. 2012, 11, 1686-1695
13. 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, 207-214
14. Lam, H.; Deutsch, E. W.; Aebersold, R. Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics J. Proteome Res. 2010, 9, 605-610
15. Kim, S.; Gupta, N.; Pevzner, P. A. Spectral probabilities and generating functions of tandem mass spectra: A strike against decoy databases J. Proteome Res. 2008, 7, 3354-3363
16. Gupta, N.; Bandeira, N.; Keich, U.; PA, P. Target-decoy approach and false discovery rate: when things may go wrong J. Am. Soc. Mass Spectrom. 2011, 22, 1111-1120
17. Venable, J.; Yates, J. Impact of ion trap tandem mass spectra variability on the identification of peptides Anal. Chem. 2004, 76, 2928-2937
18. Paulovich, A. G. Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance Mol. Cell Proteomics 2010, 9, 242-254
19. Tabb, D. L. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry J. Proteome Res. 2010, 9, 761-776
20. Rudomin, E. L.; Carr, S. A.; Jaffe, J. D. Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx) J. Proteome Res. 2009, 8, 3154-3160
21. Roepstorff, P.; Fohlman, J. Proposal for a common nomenclature for sequence ions in mass spectra of peptides Biomed. Mass Spectrom. 1984, 11, 601
22. Bandeira, N.; Tsur, D.; Frank, A.; Pevzner, P. Protein Identification via spectral networks analysis Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 6140-6145
23. Lam, H.; Aebersold, R. Spectral library searching for peptide identification via tandem MS Methods Mol. Biol. 2010, 604, 95-103