Research Article

FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification

  1. Alexandre Gattiker1,
  2. Willy V. Bienvenut2,
  3. Amos Bairoch1,
  4. Elisabeth Gasteiger1,*

Article first published online: 4 NOV 2002

DOI: 10.1002/1615-9861(200210)2:10<1435::AID-PROT1435>3.0.CO;2-9

Issue

PROTEOMICS

PROTEOMICS

Special Issue: The Application of Bioinfomatics to Mass Spectrometry

Volume 2, Issue 10, pages 1435–1444, October 2002

Additional Information

How to Cite

Gattiker, A., Bienvenut, W. V., Bairoch, A. and Gasteiger, E. (2002), FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification. PROTEOMICS, 2: 1435–1444. doi: 10.1002/1615-9861(200210)2:10<1435::AID-PROT1435>3.0.CO;2-9

Author Information

  1. 1

    Swiss Institute of Bioinformatics, Geneva, Switzerland

  2. 2

    Central Clinical Chemistry Laboratory, Geneva University Hospital, Geneva, Switzerland

*Swiss Institute of Bioinformatics, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland Fax: +41-22-7025858

Publication History

  1. Issue published online: 4 NOV 2002
  2. Article first published online: 4 NOV 2002
  3. Manuscript Received:

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

Get PDF (281K)

Keywords:

  • Endoproteinase;
  • Mass spectrometry;
  • Peptide mass fingerprint;
  • Protein identification;
  • Unspecific cleavage

Abstract

FindPept (http://www.expasy.org/tools/findpept.html) is a software tool designed to identify the origin of peptide masses obtained by peptide mass fingerprinting which are not matched by existing protein identification tools. It identifies masses resulting from unspecific proteolytic cleavage, missed cleavage, protease autolysis or keratin contaminants. It also takes into account post-translational modifications derived from the annotation of the SWISS-PROT database or supplied by the user, and chemical modifications of peptides. Based on a number of experimental examples, we show that the commonly held rules for the specificity of tryptic cleavage are an oversimplification, mainly because of effects of neighboring residues, experimental conditions, and contaminants present in the enzyme sample.

Get PDF (281K)