decryptM 2.0 - Dataset

This is the data repository containing 17 million peptidoform dose-response curves for 133 clinical kinase inhibitors across 5 different cell lines (A204, A431, MESSA, SKES1, SKLMS1). Results files (.txt) and dashboards (.html) are bundled by cell lines. A dataset overview is available in the Supplement folder Table S1. The data dictionary explains the columns of the result files. Briefly, 133 kinase inhibitors were titrated with 10 increasing doses and 1 vehicle control in 5 different cell lines. Depending on the on- and off-target affinities to kinases, phosphorylation changes will be a function of the applied dose. After treatment, proteoforms were extracted and digested into peptidoforms with trypsin. The 11 treatments of one experiment are TMT-multiplexed, and low-abundant phosphorylated peptidoforms were enriched by IMAC. The phosphorylated sample was then bRP fractionated into 6 fractions. Each fraction was LC-MS3 measured with an 80-min gradient. After identifying and localizing peptidoforms at 1% FDR, dose-response profiles were fitted and statistically evaluated using CurveCurator. This repository hosts these output files. Please note that we have already aggregated duplicates by reporting the most confident MS2/MS3 pair. All non-phosphorylated peptidoforms have been removed here. If a TMT channel is missing, it was excluded from the analysis because it did not pass our quality control criteria. All MS raw data is available at PRIDE (PXD065258, PXD065178, PXD065229, PXD065236, PXD065212). For more information, we refer to the original paper by Bayer et al.