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. Data were produced from the IPM-based QTRP (quantitative thiol reactivity profiling) applications in various species, including Arabidopsis thaliana, Escherichia coli, Homo sapiens, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Psedomonas syringae, and Mus musculus. IPM is a clickable thiol reactive reagent with the iodoacetamide warhead.