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Quantifying Homologous Proteins and Proteoforms.
Malioutov D, Chen T, Airoldi E, Jaffe J, Budnik B, Slavov N. Malioutov D, et al. Among authors: Jaffe J. Mol Cell Proteomics. 2019 Jan;18(1):162-168. doi: 10.1074/mcp.TIR118.000947. Epub 2018 Oct 3. Mol Cell Proteomics. 2019. PMID: 30282776 Free PMC article.
MapQuant: open-source software for large-scale protein quantification.
Leptos KC, Sarracino DA, Jaffe JD, Krastins B, Church GM. Leptos KC, et al. Among authors: Jaffe JD. Proteomics. 2006 Mar;6(6):1770-82. doi: 10.1002/pmic.200500201. Proteomics. 2006. PMID: 16470651
PEPPeR, a platform for experimental proteomic pattern recognition.
Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA. Jaffe JD, et al. Mol Cell Proteomics. 2006 Oct;5(10):1927-41. doi: 10.1074/mcp.M600222-MCP200. Epub 2006 Jul 19. Mol Cell Proteomics. 2006. PMID: 16857664 Free PMC article.
Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules.
Peach SE, Rudomin EL, Udeshi ND, Carr SA, Jaffe JD. Peach SE, et al. Among authors: Jaffe JD. Mol Cell Proteomics. 2012 May;11(5):128-37. doi: 10.1074/mcp.M111.015941. Epub 2012 Mar 21. Mol Cell Proteomics. 2012. PMID: 22442256 Free PMC article.
Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA. Udeshi ND, et al. Among authors: Jaffe JD. Mol Cell Proteomics. 2012 May;11(5):148-59. doi: 10.1074/mcp.M111.016857. Epub 2012 Apr 14. Mol Cell Proteomics. 2012. PMID: 22505724 Free PMC article.
Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator.
Maier VK, Feeney CM, Taylor JE, Creech AL, Qiao JW, Szanto A, Das PP, Chevrier N, Cifuentes-Rojas C, Orkin SH, Carr SA, Jaffe JD, Mertins P, Lee JT. Maier VK, et al. Among authors: Jaffe JD. Mol Cell Proteomics. 2015 Jun;14(6):1435-46. doi: 10.1074/mcp.M114.044586. Epub 2015 Feb 13. Mol Cell Proteomics. 2015. PMID: 25680957 Free PMC article.
Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow.
Svinkina T, Gu H, Silva JC, Mertins P, Qiao J, Fereshetian S, Jaffe JD, Kuhn E, Udeshi ND, Carr SA. Svinkina T, et al. Among authors: Jaffe JD. Mol Cell Proteomics. 2015 Sep;14(9):2429-40. doi: 10.1074/mcp.O114.047555. Epub 2015 May 7. Mol Cell Proteomics. 2015. PMID: 25953088 Free PMC article.
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