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A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases.
Sadygov RG, Yates JR 3rd. Sadygov RG, et al. Anal Chem. 2003 Aug 1;75(15):3792-8. doi: 10.1021/ac034157w. Anal Chem. 2003. PMID: 14572045
Shotgun identification of protein modifications from protein complexes and lens tissue.
MacCoss MJ, McDonald WH, Saraf A, Sadygov R, Clark JM, Tasto JJ, Gould KL, Wolters D, Washburn M, Weiss A, Clark JI, Yates JR 3rd. MacCoss MJ, et al. Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):7900-5. doi: 10.1073/pnas.122231399. Proc Natl Acad Sci U S A. 2002. PMID: 12060738 Free PMC article.
Code developments to improve the efficiency of automated MS/MS spectra interpretation.
Sadygov RG, Eng J, Durr E, Saraf A, McDonald H, MacCoss MJ, Yates JR 3rd. Sadygov RG, et al. J Proteome Res. 2002 May-Jun;1(3):211-5. doi: 10.1021/pr015514r. J Proteome Res. 2002. PMID: 12645897
A correlation algorithm for the automated quantitative analysis of shotgun proteomics data.
MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR 3rd. MacCoss MJ, et al. Anal Chem. 2003 Dec 15;75(24):6912-21. doi: 10.1021/ac034790h. Anal Chem. 2003. PMID: 14670053
Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases.
Sadygov RG, Liu H, Yates JR. Sadygov RG, et al. Anal Chem. 2004 Mar 15;76(6):1664-71. doi: 10.1021/ac035112y. Anal Chem. 2004. PMID: 15018565
A model for random sampling and estimation of relative protein abundance in shotgun proteomics.
Liu H, Sadygov RG, Yates JR 3rd. Liu H, et al. Among authors: sadygov rg. Anal Chem. 2004 Jul 15;76(14):4193-201. doi: 10.1021/ac0498563. Anal Chem. 2004. PMID: 15253663
MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications.
McDonald WH, Tabb DL, Sadygov RG, MacCoss MJ, Venable J, Graumann J, Johnson JR, Cociorva D, Yates JR 3rd. McDonald WH, et al. Among authors: sadygov rg. Rapid Commun Mass Spectrom. 2004;18(18):2162-8. doi: 10.1002/rcm.1603. Rapid Commun Mass Spectrom. 2004. PMID: 15317041
Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book.
Sadygov RG, Cociorva D, Yates JR 3rd. Sadygov RG, et al. Nat Methods. 2004 Dec;1(3):195-202. doi: 10.1038/nmeth725. Nat Methods. 2004. PMID: 15789030 Review.
Central limit theorem as an approximation for intensity-based scoring function.
Sadygov R, Wohlschlegel J, Park SK, Xu T, Yates JR 3rd. Sadygov R, et al. Anal Chem. 2006 Jan 1;78(1):89-95. doi: 10.1021/ac051206r. Anal Chem. 2006. PMID: 16383314
ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.
Sadygov RG, Maroto FM, Hühmer AF. Sadygov RG, et al. Anal Chem. 2006 Dec 15;78(24):8207-17. doi: 10.1021/ac060923y. Anal Chem. 2006. PMID: 17165809
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