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This Week in Cell: Jul 27, 2016

Members of the Clinical Proteomic Tumor Analysis Consortium report on proteomic patterns detected through mass spectrometry-based analyses of 169 high-grade serous ovarian carcinomas. The team combined those proteomic data with information from genomic analyses of the tumors, done for the Cancer Genome Atlas project, to look at the proteomic consequences of somatic mutations, copy number changes, and other cancer-related alterations. "In addition to providing a valuable resource," the group writes, "these findings provide a view of how the somatic genome drives the cancer proteome and associations between protein and post-translational modification levels and clinical outcomes in [high-grade serous carcinomas]."

An international team led by investigators at the Wellcome Trust Sanger Institute presents a pharmacogenomic investigation of alterations identified in human cancers. Using 1,001 human cancer cell lines, the researchers looked for changes in response to 265 drugs in the presence of somatic mutations, copy number changes, DNA methylation profiles, and gene expression patterns uncovered in analyses of nearly 11,300 tumors for efforts such as TCGA or the International Cancer Genome Consortium. Indeed, more than 80 percent of the 1,273 'cancer functional events' detected across the cancer types turned up in one or more cell lines, with many of those alterations affecting drug sensitivity or resistance — data they used to model drug response in the presence of mutation combinations.

Researchers from the US, Switzerland, and Hong Kong describe the Human SRMAtlas, a collection of targeted selected reaction monitoring mass spec assays for quantifying human proteins and peptides present in organs, tissues, cells, and body fluids in the human body. In addition to offering a means of quantifying most of the 20,277 annotated human proteins, the team demonstrated that independent, complementary assays included in SRMAtlas could pick up nearly 166,200 proteotypic synthetic peptides. "We expect that this resource will significantly advance protein based experimental biology because any human protein can now, in principle, be quantified in any sample," the study's authors wrote.