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Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.
Choi H, Nesvizhskii AI. Choi H, et al. Among authors: nesvizhskii ai. J Proteome Res. 2008 Jan;7(1):254-65. doi: 10.1021/pr070542g. Epub 2007 Dec 27. J Proteome Res. 2008. PMID: 18159924
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: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts.
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):426-7. doi: 10.1074/mcp.D300002-MCP200. Epub 2003 Jun 25. Mol Cell Proteomics. 2003. PMID: 12832456
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.
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.
Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, Kregenow F, Lee H, Lin B, Martin D, Ranish JA, Rawlings DJ, Samelson LE, Shiio Y, Watts JD, Wollscheid B, Wright ME, Yan W, Yang L, Yi EC, Zhang H, Aebersold R. Desiere F, et al. Among authors: nesvizhskii ai. Genome Biol. 2005;6(1):R9. doi: 10.1186/gb-2004-6-1-r9. Epub 2004 Dec 10. Genome Biol. 2005. PMID: 15642101 Free PMC article.
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories.
Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K. Martens L, et al. Among authors: nesvizhskii ai. Proteomics. 2005 Aug;5(13):3501-5. doi: 10.1002/pmic.200401302. Proteomics. 2005. PMID: 16041670
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.
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