Quantitative proteome landscape of the NCI-60 cancer cell lines

Tiannan Guo, Augustin Luna, Vinodh N. Rajapakse, Ching Chiek Koh, Zhicheng Wu, Wei Liu, Yaoting Sun, Huanhuan Gao, Michael P. Menden, Chao Xu, Laurence Calzone, Loredana Martignetti (+27 others)
2019 iScience  
Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure cycling technology and SWATH mass spectrometry. We developed the DIA-expert software to curate and visualize the SWATH data, leading to reproducible detection of over 3,100 SwissProt proteotypic proteins and systematic quantification of pathway activities. Stoichiometric relationships of interacting proteins for DNA replication, repair, the chromatin remodeling NuRD complex, β-catenin, RNA metabolism, and
more » ... prefoldins are more evident than that at the mRNA level. The data are available in CellMiner (discover.nci.nih.gov/cellminercdb and discover.nci.nih.gov/cellminer), allowing casual users to test hypotheses and perform integrative, cross-database analyses of multi-omic drug response correlations for over 20,000 drugs. We demonstrate the value of proteome data in predicting drug response for over 240 clinically relevant chemotherapeutic and targeted therapies. In summary, we present a novel proteome resource for the NCI-60, together with relevant software tools, and demonstrate the benefit of proteome analyses.
doi:10.1016/j.isci.2019.10.059 pmid:31733513 pmcid:PMC6889472 fatcat:j4w2gpvfvbhydmhouvykp5quba