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Proteomics Platform

Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2.

Greulich H, Kaplan B, Mertins P, et al. Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2. Proc Natl Acad Sci U S A. 2012;109(36):14476-81. doi:10.1073/pnas.1203201109

ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression.

Abdel-Wahab O, Adli M, LaFave LM, et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell. 2012;22(2):180-93. doi:10.1016/j.ccr.2012.06.032

Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL.

Wen Q, Goldenson B, Silver SJ, et al. Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL. Cell. 2012;150(3):575-89. doi:10.1016/j.cell.2012.06.032

iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.

Mertins P, Udeshi ND, Clauser KR, et al. iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics. Mol Cell Proteomics. 2012;11(6):M111.014423. doi:10.1074/mcp.M111.014423

Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma.

Kuhn E, Whiteaker JR, Mani DR, et al. Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol Cell Proteomics. 2012;11(6):M111.013854. doi:10.1074/mcp.M111.013854

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

Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.

Udeshi ND, Mani DR, Eisenhaure T, et al. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol Cell Proteomics. 2012;11(5):148-59. doi:10.1074/mcp.M111.016857

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. Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. Mol Cell Proteomics. 2012;11(5):128-37. doi:10.1074/mcp.M111.015941

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