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Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling.
Choi H, Ghosh D, Nesvizhskii AI. Choi H, et al. Among authors: nesvizhskii ai. J Proteome Res. 2008 Jan;7(1):286-92. doi: 10.1021/pr7006818. Epub 2007 Dec 14. J Proteome Res. 2008. PMID: 18078310
Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors.
Djomehri SI, Gonzalez ME, da Veiga Leprevost F, Tekula SR, Chang HY, White MJ, Cimino-Mathews A, Burman B, Basrur V, Argani P, Nesvizhskii AI, Kleer CG. Djomehri SI, et al. Among authors: nesvizhskii ai. Nat Commun. 2020 Apr 7;11(1):1723. doi: 10.1038/s41467-020-15283-z. Nat Commun. 2020. PMID: 32265444 Free PMC article.
Experimental protein mixture for validating tandem mass spectral analysis.
Keller A, Purvine S, Nesvizhskii AI, Stolyar S, Goodlett DR, Kolker E. Keller A, et al. Among authors: nesvizhskii ai. OMICS. 2002;6(2):207-12. doi: 10.1089/153623102760092805. OMICS. 2002. PMID: 12143966
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Keller A, et al. Among authors: nesvizhskii ai. Anal Chem. 2002 Oct 15;74(20):5383-92. doi: 10.1021/ac025747h. Anal Chem. 2002. PMID: 12403597
The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation.
von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. von Haller PD, et al. Among authors: nesvizhskii ai. Mol Cell Proteomics. 2003 Jul;2(7):428-42. doi: 10.1074/mcp.M300041-MCP200. Epub 2003 Jun 25. Mol Cell Proteomics. 2003. PMID: 12832459
A statistical model for identifying proteins by tandem mass spectrometry.
Nesvizhskii AI, Keller A, Kolker E, Aebersold R. Nesvizhskii AI, et al. Anal Chem. 2003 Sep 1;75(17):4646-58. doi: 10.1021/ac0341261. Anal Chem. 2003. PMID: 14632076
Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS.
Nesvizhskii AI, Aebersold R. Nesvizhskii AI, et al. Drug Discov Today. 2004 Feb 15;9(4):173-81. doi: 10.1016/S1359-6446(03)02978-7. Drug Discov Today. 2004. PMID: 14960397 Review.
Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis.
Malmström J, Lee H, Nesvizhskii AI, Shteynberg D, Mohanty S, Brunner E, Ye M, Weber G, Eckerskorn C, Aebersold R. Malmström J, et al. Among authors: nesvizhskii ai. J Proteome Res. 2006 Sep;5(9):2241-9. doi: 10.1021/pr0600632. J Proteome Res. 2006. PMID: 16944936
Protein identification by tandem mass spectrometry and sequence database searching.
Nesvizhskii AI. Nesvizhskii AI. Methods Mol Biol. 2007;367:87-119. doi: 10.1385/1-59745-275-0:87. Methods Mol Biol. 2007. PMID: 17185772 Review.
Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS.
Yoo C, Patwa TH, Kreunin P, Miller FR, Huber CG, Nesvizhskii AI, Lubman DM. Yoo C, et al. Among authors: nesvizhskii ai. J Mass Spectrom. 2007 Mar;42(3):312-34. doi: 10.1002/jms.1163. J Mass Spectrom. 2007. PMID: 17206599 Free PMC article.
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