Identification of post-translational modified proteins has become one of the central issue of current proteomics. Spectral library search is a new and promising computational approach to mass spectrometry-based protein identification. However, its potential in identification of unanticipated post-translational modifications (PTMs) has rarely been explored.

pMatch is a spectral library search tool, which is deliberately designed for the open search mode, and has the following key features:

(1) The spectra in library are optimized with the full peptide sequence information to better tolerate the peptide fragmentation pattern variations caused by some PTM(s).

(2) A new scoring system is devised, which uses charge-dependent mass shifts for peak matching and combines a probability-based model with the general spectral dot-product for scoring.

(3) A target-decoy strategy is used for false discovery rate control.


pMatch is written in C++. Please click the link below to download pMatch executables:

        pMatch Version 1.5 for Windows (new)

        pMatch Version 1.4 for Windows (new)


    v1.5 Release (2012.02)  

   ---- An alternative version of pMatch with GUI.

  ---- pMatch User Guide for the new version.

    v1.4 Release (2011.03)  

   ---- Bugs regarding pBuild's spectra result file format are fixed.

  ---- Software functional modules are reorganized.

    v1.3 Release (2011.02)  

   ---- Multi dataset process is supported.

  ---- Problems for MGF suport in v1.2 are fixed.

    v1.2 Release (2010.11) 

   ---- pBuild's spectra result format is supported.

  ---- DTAS tandem MS spectral format is supported.

    v1.1 Release (2010.07) 

   ---- Library construction supports pepXML format. To be more specific, for the reference library construction, pMatch imploys the search results of previously identified spectra in pepXML format, which have been analyzed by PeptideProhpet (function avalable in  TPP).


Ding Ye, Yan Fu*, Ruixiang Sun*, Haipeng Wang, Zuofei Yuan, Hao Chi and Simin He. Open MS/MS Spectral Library Search to Identify Unanticipated Post-Translational Modifications and Increase Spectral Identification Rate. The 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010). Bioinformatics, 26(12):i399-i406, 2010.


Our reserch focus on algorithm and software development of MS-based proteomics. For more information, please visit our website.

Our affiliations:
        Institute of Computing Technology, Chinese Academy of Sciences
        Graduate University of Chinese Academy of Sciences


Address:  No.6 Kexueyuan South Road,
                  Haidian District, Beijing,China
Postcode: 100190
Tel: 86-10-62601016
Fax: 86-10-62601356

Any problem with pMatch or this website, please contact:

Ding Ye : dye (AT)

Yan Fu : yfu (AT)

Rui-Xiang Sun : rxsun (AT)


This work was supported by the National Natural Science Foundation of China under Grant No. 30900262, the CAS Knowledge Innovation Program under Grant No. KGGX1-YW-13, the National Key Basic Research & Development Program (973) of China under Grant No. 2010CB912701, and the National High Technology Research and Development Program (863) of China under Grant Nos. 2007AA02Z315, 2008AA02Z309.

  Copyright (C) 2010 by Bioinformatics Group, Institute of Computing Technology, CAS