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Validation of tandem mass spectrometry database search results using DTASelect.
Cociorva D, L Tabb D, Yates JR. Cociorva D, et al. Curr Protoc Bioinformatics. 2007 Jan;Chapter 13:Unit 13.4. doi: 10.1002/0471250953.bi1304s16. Curr Protoc Bioinformatics. 2007. PMID: 18428785
ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity.
Xu T, Park SK, Venable JD, Wohlschlegel JA, Diedrich JK, Cociorva D, Lu B, Liao L, Hewel J, Han X, Wong CCL, Fonslow B, Delahunty C, Gao Y, Shah H, Yates JR 3rd. Xu T, et al. Among authors: cociorva d. J Proteomics. 2015 Nov 3;129:16-24. doi: 10.1016/j.jprot.2015.07.001. Epub 2015 Jul 11. J Proteomics. 2015. PMID: 26171723 Free PMC article.
Motif-specific sampling of phosphoproteomes.
Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd. Ruse CI, et al. Among authors: cociorva d. J Proteome Res. 2008 May;7(5):2140-50. doi: 10.1021/pr800147u. J Proteome Res. 2008. PMID: 18452278 Free PMC article.
Proteomics of Pyrococcus furiosus (Pfu): Identification of Extracted Proteins by Three Independent Methods.
Wong CC, Cociorva D, Miller CA, Schmidt A, Monell C, Aebersold R, Yates JR 3rd. Wong CC, et al. Among authors: cociorva d. J Proteome Res. 2013 Feb 1;12(2):763-70. doi: 10.1021/pr300840j. Epub 2013 Jan 18. J Proteome Res. 2013. PMID: 23298259 Free PMC article.
Toward objective evaluation of proteomic algorithms.
Yates JR 3rd, Park SK, Delahunty CM, Xu T, Savas JN, Cociorva D, Carvalho PC. Yates JR 3rd, et al. Among authors: cociorva d. Nat Methods. 2012 Apr 27;9(5):455-6. doi: 10.1038/nmeth.1983. Nat Methods. 2012. PMID: 22543378 Free PMC article. No abstract available.
Comparison of different signal thresholds on data dependent sampling in Orbitrap and LTQ mass spectrometry for the identification of peptides and proteins in complex mixtures.
Wong CC, Cociorva D, Venable JD, Xu T, Yates JR 3rd. Wong CC, et al. Among authors: cociorva d. J Am Soc Mass Spectrom. 2009 Aug;20(8):1405-14. doi: 10.1016/j.jasms.2009.04.007. Epub 2009 Apr 18. J Am Soc Mass Spectrom. 2009. PMID: 19467883 Free PMC article.
Quantitative mass spectrometry identifies insulin signaling targets in C. elegans.
Dong MQ, Venable JD, Au N, Xu T, Park SK, Cociorva D, Johnson JR, Dillin A, Yates JR 3rd. Dong MQ, et al. Among authors: cociorva d. Science. 2007 Aug 3;317(5838):660-3. doi: 10.1126/science.1139952. Science. 2007. PMID: 17673661
Optimization of mass spectrometry-compatible surfactants for shotgun proteomics.
Chen EI, Cociorva D, Norris JL, Yates JR 3rd. Chen EI, et al. Among authors: cociorva d. J Proteome Res. 2007 Jul;6(7):2529-38. doi: 10.1021/pr060682a. Epub 2007 May 27. J Proteome Res. 2007. PMID: 17530876 Free PMC article.
Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra.
Venable JD, Xu T, Cociorva D, Yates JR 3rd. Venable JD, et al. Among authors: cociorva d. Anal Chem. 2006 Mar 15;78(6):1921-9. doi: 10.1021/ac051636h. Anal Chem. 2006. PMID: 16536429
Performance of a linear ion trap-Orbitrap hybrid for peptide analysis.
Yates JR, Cociorva D, Liao L, Zabrouskov V. Yates JR, et al. Among authors: cociorva d. Anal Chem. 2006 Jan 15;78(2):493-500. doi: 10.1021/ac0514624. Anal Chem. 2006. PMID: 16408932
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