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Proteomics Platform

Modification site localization scoring: strategies and performance.

Chalkley RJ, Clauser KR. Modification site localization scoring: strategies and performance. Mol Cell Proteomics. 2012;11(5):3-14. doi:10.1074/mcp.R111.015305

The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.

Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO. The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Mol Cell Proteomics. 2012;11(4):M111.014647. doi:10.1074/mcp.M111.014647

Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics.

Mani DR, Abbatiello SE, Carr SA. Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics. BMC Bioinformatics. 2012;13 Suppl 16:S9. doi:10.1186/1471-2105-13-S16-S9

Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers.

Burgener A, Rahman S, Ahmad R, et al. Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers. J Proteome Res. 2011;10(11):5139-49. doi:10.1021/pr200596r

A face in the crowd: recognizing peptides through database search.

Eng JK, Searle BC, Clauser KR, Tabb DL. A face in the crowd: recognizing peptides through database search. Mol Cell Proteomics. 2011;10(11):R111.009522. doi:10.1074/mcp.R111.009522

Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation.

Tucker EJ, Hershman SG, Köhrer C, et al. Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation. Cell Metab. 2011;14(3):428-34. doi:10.1016/j.cmet.2011.07.010

STK33 kinase activity is nonessential in KRAS-dependent cancer cells.

Babij C, Zhang Y, Kurzeja RJ, et al. STK33 kinase activity is nonessential in KRAS-dependent cancer cells. Cancer Res. 2011;71(17):5818-26. doi:10.1158/0008-5472.CAN-11-0778

Clustering with position-specific constraints on variance: applying redescending M-estimators to label-free LC-MS data analysis.

Frühwirth R, Mani DR, Pyne S. Clustering with position-specific constraints on variance: applying redescending M-estimators to label-free LC-MS data analysis. BMC Bioinformatics. 2011;12:358. doi:10.1186/1471-2105-12-358

Status and prospects for discovery and verification of new biomarkers of cardiovascular disease by proteomics.

Gerszten RE, Asnani A, Carr SA. Status and prospects for discovery and verification of new biomarkers of cardiovascular disease by proteomics. Circ Res. 2011;109(4):463-74. doi:10.1161/CIRCRESAHA.110.225003

Quantification of proteins using peptide immunoaffinity enrichment coupled with mass spectrometry.

Zhao L, Whiteaker JR, Pope ME, et al. Quantification of proteins using peptide immunoaffinity enrichment coupled with mass spectrometry. J Vis Exp. 2011;(53). doi:10.3791/2812