Skip to content


Folders and files

Last commit message
Last commit date

Latest commit



19 Commits

Repository files navigation


PepQuery: a targeted peptide search engine for identifying or validating known and novel peptides of interest in MS-based proteomics data.

Web server:

PepQuery can be used in two ways:

  1. Online version: search a peptide of interest in curated large-scale proteomics MS/MS datasets;
  2. Standalone version: batch search a list of peptides in any MS/MS datasets.

How to cite:

Wen, B., et al. (2019). "PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations." Genome research 29(3): 485-493. Manuscript

Wen, B., Li, K., Zhang, Y. et al. (2020). "Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis." Nature Communications 11, 1759. Manuscript

Wen, B., Zhang, B. (2023) PepQuery2 democratizes public MS proteomics data for rapid peptide searching. Nature Communications 14, 2213. Manuscript