Erratum: On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics (Journal of Proteome Research (2011) 10 (2671-2678) DOI: 10.1021/pr1012619);On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics

Journal of Proteome Research

Volumn 10, Issue 5, 2011, Pages 2671-2678

  Granholm, Viktor ^a   Noble, William Stafford ^b   Käll, Lukas ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

calibration; database search software; p value; peptide identification; shotgun proteomics; standard protein mix

Indexed keywords

PROTEIN;

ARTICLE; CALIBRATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONTENT; PROTEOMICS; SCORING SYSTEM; STATISTICAL ANALYSIS;

EID: 79955870431     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr200517n     Document Type: Erratum

References (23)

1. Eng, J.; McCormack, A.; Yates, J.; 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, 976-989
2. Craig, R.; Beavis, R. TANDEM: matching proteins with tandem mass spectra Bioinformatics 2004, 921
3. Moore, R.; Young, M.; Lee, T. Qscore: an algorithm for evaluating SEQUEST database search results J. Am. Soc. Mass Spectrom. 2002, 13, 378-386 (Pubitemid 34280088)
4. Keller, A.; Purvine, S.; Nesvizhskii, A.; Stolyar, S.; Goodlett, D.; Kolker, E. Experimental protein mixture for validating tandem mass spectral analysis OMICS: J. Integr. Biol. 2002, 6, 207-212 (Pubitemid 35278428)
5. Keller, A.; Nesvizhskii, A.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 74, 5383-5392 (Pubitemid 35215372)
6. Nesvizhskii, A.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry Anal. Chem. 2003, 75, 4646-4658 (Pubitemid 37082259)
7. Huttlin, E. L.; Hegeman, A. D.; Harms, A. C.; Sussman, M. R. Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy J. Proteome Res. 2007, 6, 392-398 (Pubitemid 46173692)
8. Choi, H.; Ghosh, D.; Nesvizhskii, A. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling J. Proteome Res. 2007, 7, 286-292 (Pubitemid 351171141)
9. Choi, H.; Nesvizhskii, A. Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics J. Proteome Res. 2008, 7, 254
10. Bell, A.; Deutsch, E.; Au, C.; Kearney, R.; Beavis, R.; Sechi, S.; Nilsson, T.; Bergeron, J.; Beardslee, T.; Chappell, T.; Bell, A. W.; Deutsch, E. W.; Au, C. E.; Kearney, R. E.; Beavis, R.; Sechi, S.; Nilsson, T.; Bergeron, J. J. M.; Beardslee, T. A.; Chappell, T. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics Nat. Methods 2009, 6, 423-430
11. Paulovich, A.; Billheimer, D.; Ham, A.; Vega-Montoto, L.; Rudnick, P.; Tabb, D.; Wang, P.; Blackman, R.; Bunk, D.; Cardasis, H.; Paulovich, A. G.; Billheimer, D.; Ham, A. J. L.; Vega-Montoto, L.; Rudnick, P. A.; Tabb, D. L.; Wang, P.; Blackman, R. K.; Bunk, D. M.; Cardasis, H. L. Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance Mol. Cell. Proteomics 2010, 9, 242
12. Tabb, D.; Vega-Montoto, L.; Rudnick, P.; Variyath, A.; Ham, A.; Bunk, D.; Kilpatrick, L.; Billheimer, D.; Blackman, R.; Cardasis, H.; Tabb, D. L.; VegaMontoto, L.; Rudnick, P. A.; Variyath, A. M.; Ham, A. J. L.; Bunk, D. M.; Kilpatrick, L. E.; Billheimer, D. D.; Blackman, R. K.; Cardasis, H. L. Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography- Tandem Mass Spectrometry J. Proteome Res. 2009, 9, 761-776
13. Everett, L.; Bierl, C.; Master, S. Unbiased Statistical Analysis for Multi-Stage Proteomic Search Strategies J. Proteome Res. 2010, 9, 700-707
14. Yang, C.; Yang, C.; Yu, W. A Regularized Method for Peptide Quantification J. Proteome Res. 2010, 9, 2705-2712
15. Klimek, J.; Eddes, J.; Hohmann, L.; Jackson, J.; Peterson, A.; Letarte, S.; Gafken, P.; Katz, J.; Mallick, P.; Lee, H.; Klimek, J.; Eddes, J. S.; Hohmann, L.; Jackson, J.; Peterson, A.; Letarte, S.; Gafken, P. R.; Katz, J. E.; Mallick, P.; Lee, H. The standard protein mix database: a diverse data set to assist in the production of improved peptide and protein identification software tools J. Proteome Res. 2008, 7, 96-103 (Pubitemid 351171120)
16. Käll, L.; Canterbury, J.; Weston, J.; Noble, W.; MacCoss, M. Semi-supervised learning for peptide identification from shotgun proteomics datasets Nat. Methods 2007, 4, 923-925 (Pubitemid 350042380)
17. McDonald, W.; Tabb, D.; Sadygov, R.; MacCoss, M.; Venable, J.; Graumann, J.; Johnson, J.; Cociorva, D.; Yates, J., III MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications Rapid Commun. Mass Spectrom. 2004, 18, 2162-2168 (Pubitemid 39222458)
18. Park, C.; Käll, L.; Klammer, A.; MacCoss, M.; Noble, W. Rapid and accurate peptide identification from tandem mass spectra J. Proteome Res. 2008, 7, 3022
19. Kim, S.; Mischerikow, N.; Bandeira, N.; Navarro, J.; Wich, L.; Mohammed, S.; Heck, A.; Pevzner, P. The generating function of CID, ETD and CID/ETD pairs of tandem mass spectra: Applications to database search Mol. Cell. Proteomics 2010, 9 (12) 2840-52
20. Keller, A.;; Eng, J.;; Zhang, N.;; Li, X.;; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats Mol. Syst. Biol. 2005, doi: 10.1038/msb4100024.
21. Davison, A. C.; Hinkley, D. V. Bootstrap Methods and Their Application; Cambridge University Press: Cambridge, 1997.
22. Gupta, N.; Pevzner, P. False discovery rates of protein identifications: a strike against the two-peptide rule J. Proteome Res. 2009, 8, 4173-4181
23. Ŝ'idák, Z. Rectangular confidence regions for the means of multivariate normal distributions J. Am. Stat. Assoc. 1967, 62, 626-633