日本質量分析学会 第66回質量分析総合討論会

Program

Oral Sessions

Day 4, May 18(Fri.) 15:05-15:25 Room C (Seiun 2)

Integrated characterisation of human cancer cell lines using public proteomics data

(EMBL-EBI)
oAndrew Jarnuczak, Juan Vizcaino

Molecular profiles of large collections of cancer cell lines have been previously characterised using various omics techniques. Quantitative proteomics profiling, however, has so far been confined to studies focusing on a relatively small subset of available cell lines.
Here we present an integrated analysis of 148 cancer cell lines based on over three thousand individual LC-MS/MS runs from publicly available quantitative proteomics datasets. The combined analysis provided identification of 16,306 UniProt protein groups at 1% PSM and 1% protein FDR. By employing a robust normalisation strategy, we generated complete expression profiles across all the cell lines for over 6,000 proteins. Those profiles are used to identify differentially expressed proteins and to classify the cell lines into coherent clusters, related to their lineage. We also integrated proteomics data with transcriptome measurements in the corresponding cell lines. We observed a positive correlation between mRNA and protein expression, ranging from 0.4 to 0.7, with no apparent differences between the cell lines studied.
We believe that this integrated study provides novel insights into the differences between cell lines, and serves as a rich resource of reference protein expression for the cancer research community.