Cancer Cell Line Encyclopedia Proteomics

We recently reported the quantitative proteomics of 375 samples as part of the cancer cell line encyclopedia nusinow et al 2020 1.

Cancer cell line encyclopedia proteomics. The experiment was performed in multiplex format with 9 biological samples per plex and one common sample to normalize between plexes. The cancer cell line encyclopedia ccle is an effort to generate large scale profiling datasets across nearly 1 000 cell lines from diverse tissue lineages. Quantitative proteomes of 375 cancer cell lines for the cancer cell line encyclopedia ccle reveal correlated protein expression between multiple pathways and complexes as well as associations between protein complexes and genetic features including microsatellite instability individual gene mutations and sensitivity to gene knockdowns. Over the past decade data from gene expression histone profiling.

Its original release included gene expression dna copy numbers and hybrid capture sequencing barretina et al 2012. To date large scale profiling of cell line collections including the cancer cell line encyclopedia ccle has focused primarily on genetic information whereas deep interrogation of the proteome has remained out of reach. In this publication we expand the cancer cell line encyclopedia to include quantitative proteome profiling by mass spectrometry of 375 cell lines from diverse lineages. The cancer cell line encyclopedia ccle is a catalog of nearly 1 000 human cancer cell lines that have been extensively profiled.

Here we expand the ccl. From the proteomics community there was interest about how we normalized the data as the. 2020 the broad institute of mit harvard. To further understand the metabolic diversity of cancer we profiled 225 metabolites in 928 cell lines from more than 20 cancer types in the cancer cell line encyclopedia ccle using liquid.