Pan-cancer proteomic map of 949 human cell lines

Cancer Cell. 2022 Aug 8;40(8):835-849.e8. doi: 10.1016/j.ccell.2022.06.010. Epub 2022 Jul 14.


The proteome provides unique insights into disease biology beyond the genome and transcriptome. A lack of large proteomic datasets has restricted the identification of new cancer biomarkers. Here, proteomes of 949 cancer cell lines across 28 tissue types are analyzed by mass spectrometry. Deploying a workflow to quantify 8,498 proteins, these data capture evidence of cell-type and post-transcriptional modifications. Integrating multi-omics, drug response, and CRISPR-Cas9 gene essentiality screens with a deep learning-based pipeline reveals thousands of protein biomarkers of cancer vulnerabilities that are not significant at the transcript level. The power of the proteome to predict drug response is very similar to that of the transcriptome. Further, random downsampling to only 1,500 proteins has limited impact on predictive power, consistent with protein networks being highly connected and co-regulated. This pan-cancer proteomic map (ProCan-DepMapSanger) is a comprehensive resource available at

Keywords: CRISPR-Cas9; cancer; cancer vulnerability; cell line; drug response; gene essentiality; mass spectrometry; proteomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biomarkers, Tumor / genetics
  • Cell Line
  • Humans
  • Neoplasms* / genetics
  • Proteome / metabolism
  • Proteomics* / methods


  • Biomarkers, Tumor
  • Proteome

Associated data

  • figshare/10.6084/m9.figshare.19345397