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MascotDatfile: An open-source library to fully parse and analyse MASCOT MS/MS search results

  1. Kenny Helsens1,†,
  2. Lennart Martens Dr.1,2,†,*,
  3. Joël Vandekerckhove1,
  4. Kris Gevaert1

Article first published online: 4 JAN 2007

DOI: 10.1002/pmic.200600682

Issue

PROTEOMICS

PROTEOMICS

Volume 7, Issue 3, pages 364–366, No. 3 February 2007

Additional Information

How to Cite

Helsens, K., Martens, L., Vandekerckhove, J. and Gevaert, K. (2007), MascotDatfile: An open-source library to fully parse and analyse MASCOT MS/MS search results. PROTEOMICS, 7: 364–366. doi: 10.1002/pmic.200600682

Author Information

  1. 1

    Department of Biochemistry and Medical Protein Research, Faculty of Medicine and Health Sciences, Flanders Interuniversity Institute for Biotechnology, Ghent University, Ghent, Belgium

  2. 2

    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

  1. †

    Both these authors contributed equally to this work.

*EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Fax: +44-1223-494-484

Publication History

  1. Issue published online: 2 FEB 2007
  2. Article first published online: 4 JAN 2007
  3. Manuscript Received: 8 SEP 2006

Funded by

  • the Fund for Scientific Research – Flanders, Belgium (F.W.O Vlaanderen)

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Keywords:

  • Bioinformatics;
  • Protein identification

Abstract

MS-based protein identification is an important part of both gel-based and gel-free proteome studies. The MASCOT search engine (http://www.matrixscience.com) provides one of the most popular automated algorithms for this task. Here we present an open-source software library written in Java that parses raw MASCOT results into an easily accessible and fully functional object model (http://genesis.ugent.be/MascotDatfile). Several scripts based on this library are provided as examples, allowing direct automation of important routine tasks involved in processing peptide identifications.

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