Bioinformatics

Proteome informatics I: Bioinformatics tools for processing experimental data

  1. Patricia M. Palagi Dr.1,*,
  2. Patricia Hernandez1,
  3. Daniel Walther1,
  4. Ron D. Appel1,2,3

Article first published online: 22 SEP 2006

DOI: 10.1002/pmic.200600273

Issue

PROTEOMICS

PROTEOMICS

Special Issue: PROTEOMICS REVIEWS 2006 Part II

Volume 6, Issue 20, pages 5435–5444, No. 20 October 2006

Additional Information

How to Cite

Palagi, P. M., Hernandez, P., Walther, D. and Appel, R. D. (2006), Proteome informatics I: Bioinformatics tools for processing experimental data. PROTEOMICS, 6: 5435–5444. doi: 10.1002/pmic.200600273

Author Information

  1. 1

    Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland

  2. 2

    Computer Science Department, Geneva University, Geneva, Switzerland

  3. 3

    Geneva University Hospitals, Geneva, Switzerland

*Swiss Institute of Bioinformatics CMU, 1 Michel-Servet CH-1211, Geneva 4, Switzerland Fax: +41-22-379-5858

Publication History

  1. Issue published online: 16 OCT 2006
  2. Article first published online: 22 SEP 2006
  3. Manuscript Received: 13 APR 2006

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Keywords:

  • Analysis;
  • Bioinformatics;
  • Platforms;
  • Software;
  • Tools

Abstract

Bioinformatics tools for proteomics, also called proteome informatics tools, span today a large panel of very diverse applications ranging from simple tools to compare protein amino acid compositions to sophisticated software for large-scale protein structure determination. This review considers the available and ready to use tools that can help end-users to interpret, validate and generate biological information from their experimental data. It concentrates on bioinformatics tools for 2-DE analysis, for LC followed by MS analysis, for protein identification by PMF, by peptide fragment fingerprinting and by de novo sequencing and for data quantitation with MS data. It also discloses initiatives that propose to automate the processes of MS analysis and enhance the quality of the obtained results.

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