Welcome to the PepQuery2 workshop!

PepQuery2 is a search engine for identifying or validating known and novel peptide sequences of interest in any local or publicly available mass spectrometry-based proteomics datasets. PepQuery2 exists as a Web Application and a standalone version.

The standalone version of PepQuery2 allows users to search more than one billion MS/MS data indexed in the PepQueryDB from any computers with internet access. It also supports direct analysis of user provided MS/MS data, any public datasets in PRIDE, MassIVE, jPOSTrepo and iProX, or Universal Spectrum Identifiers (USIs) from ProteomeXchange.

Here are also the presentation slides which summarise how PepQuery2 works.

Hands-on examples

Check out the Web Application section for an example of how PepQuery2 works

Check out the Standalone version section for an example of what else you can do with PepQuery2. This section also shows how the Installation of the standalone version works.

Note

For more information check out the official PepQuery2 documentation.

Contents

• Web Application
  • Preparation
  • Identifying novel peptides
• Standalone version
  • Installation
  • Identifying novel peptides

Manuscripts

Wen, Bo, Xiaojing Wang, and Bing Zhang. “PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations.” Genome research 29.3 (2019): 485-493. https://doi.org/10.1101/gr.235028.118

Wen, Bo, and Bing Zhang. “PepQuery2 democratizes public MS proteomics data for rapid peptide searching.” Nature Communications 14.1 (2023): 2213. https://doi.org/10.1038/s41467-023-37462-4