PepQuery2 democratizes public MS proteomics data for rapid peptide searching.

We present PepQuery2, which leverages a new tandem mass spectrometry (MS/MS) data indexing approach to enable ultrafast, targeted identification of novel and known peptides in any local or publicly available MS proteomics datasets. The stand-alone version of PepQuery2 allows directly searching more than one billion indexed MS/MS spectra in the PepQueryDB or any public datasets from PRIDE, MassIVE, iProX, or jPOSTrepo, whereas the web version enables users to search datasets in PepQueryDB with a user-friendly interface. We demonstrate the utilities of PepQuery2 in a wide range of applications including detecting proteomic evidence for genomically predicted novel peptides, validating novel and known peptides identified using spectrum-centric database searching, prioritizing tumor-specific antigens, identifying missing proteins, and selecting proteotypic peptides for targeted proteomics experiments. By putting public MS proteomics data directly into the hands of scientists, PepQuery2 opens many new ways to transform these data into useful information for the broad research community.