PepQuery2 democratizes public MS proteomics data for rapid peptide searching.

ABSTRACT: 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 an

SUBMITTER: Wen B 

PROVIDER: S-EPMC10113256 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature