Welcome to PepQuery

PepQuery is a universal targeted peptide search engine for identifying or validating known and novel peptides of interest in any local or publicly available mass spectrometry-based proteomics datasets. The main functions of PepQuery include:

Novel peptide identification. The input could be a peptide, protein or DNA sequence.

Known peptide or protein identification. The input could be a known peptide or a protein ID.

PSM validation. The input is a pair of peptide and spectrum ID. The peptide could be a novel or known peptide.

Searching against more than 1 billion indexed MS/MS spectra from 48 large scale human proteomics dataset through PepQuery web server or command line on a local computer with internet connection.

Directly searching proteomics datasets (raw, mgf, mzML, mzXML) from public proteomics data repositories, such as PRIDE, MassIVE, jPOSTrepo and iProX.

Support PSM validation from a USI.

Learn More

News
01/13/2023 PepQuery Web:

1. Improved handling input format error.

12/21/2022 PepQuery Web:

1. Fixed table randomly collapse issue.
2. Improved showing long dataset string in "MS/MS dataset" drop-down list.
3. Fixed a few other minor issues related to webpage.

11/23/2022 PepQuery Web:

1. Improved error message handling.
2. Fixed a bug when input sequence contains blank.
3. Improved caching with error.

08/04/2022 PepQuery Web:

1. Fixed a bug in setting DNA translation frame using the web interface.

08/02/2022 PepQuery 2.0.2:

1. Fixed a bug in accessing PepQueryDB on Windows computers.

08/01/2022 PepQuery 2.0.1:

1. Updated PepQueryDB access method. The previous version 2.0.0 is no longer able to access PepQueryDB.
2. Updated two dependent Java libraries.

05/30/2022 PepQuery 2.0.0:

1. Supported known peptide and protein identification;
2. Supported PSM validation;
3. Supported gene-centric peptide identification;
4. Supported more MS/MS data formats;
5. Supported directly searching proteomics data available in public data repositories including PRIDE, MassIVE, jPOSTrepo and iProX;
6. Supported PSM validation from a USI;
7. New indexed MS/MS spectra database (PepQueryDB) which contains more than one billion spectra;
8. All the public large scale CPTAC proteomics datasets available at PDC are included in PepQueryDB;
9. Supported searching PepQueryDB in any computer with internet connection using the standalone version;
10. Improved parameter setting: provided many predifined parameter settings for many different experiment workflows;
11. Supported downloading protein reference database on the fly when run PepQuery;
12. Supported modification setting for all the modifications in UniMod;
13. Supported isotope error setting;
14. Improved identification for phosphopeptide, acetylation (K) peptide and ubiquitination (K) peptide;
15. Web server is updated to support the latest version;
16. Improved spectrum annotation in the web server for modified peptides;
17. Updated log4j to version 2.17.2;
18. Various bug fixes and other improvements.

02/22/2021:

1. Released PepQuery version 1.6.2.

02/01/2020:

1. Released PepQuery version 1.4.1. In this version, we supported MHC ligand identification using immunopeptidomics data and fixed a few bugs.

07/28/2019:

1. Released PepQuery version 1.2.0.

10/17/2018:

1. Added a tool to support searching multiple datasets in a single run.

06/19/2018:

1. Added more than 30 MS/MS datasets for the web server. This increased the total number of MS/MS spectra more than 0.5 billion;
2. Updated PepQuery to output the best matches from the reference database searching for the spectra which matched to the input target peptides;
3. Updated web server of PepQuery to present the best matched annotated spectra from the reference database searching.

01/05/2018:

1. Updated protein reference database for dataset PASS00215_jurcat in the web server.

How to Cite

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.
Wen, Bo, Kai Li, Yun Zhang, and Bing Zhang. "Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis." Nature communications 11.1 (2020): 1-14.
Wen, Bo, and Bing Zhang. "PepQuery2 democratizes public MS proteomics data for rapid peptide searching." Nature communications 14.1 (2023): 2213.

If you have any questions, suggestions or remarks, please open an issue at Github issues tracker or reach us through Gitter or PepQuery Google Group.