Updated project metadata. Data sets are used for benchmarking, pChem, a modification-centric, blind-search tool to provide a streamlined pipeline for unbiased assessing of the performance of chemoproteomic probes. The IPM-based QTRP (quantitative thiol reactivity profiling) data sets were recorded on different LC-MS/MS instruments from three vendors. IPM is a clickable thiol reactive reagent with the iodoacetamide warhead.