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Bioinformatics Advance Access originally published online on August 6, 2008
Bioinformatics 2008 24(19):2267-2269; doi:10.1093/bioinformatics/btn413
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Peptide Finder: mapping measured molecular masses to peptides and proteins

Anastasia Alexandridou 1,2, George Th. Tsangaris 1, Konstantinos Vougas 1, Konstantina Nikita 2 and George Spyrou 1,*

1Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 115 27 Athens and 2School of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., 15780, Zografos, Athens, Greece

*To whom correspondence should be addressed.


  Abstract

Summary: The identification of unknown amino acid sequences of peptides as well as protein identification is of great significance in proteomics. Here, we present a publicly available web application that facilitates a high resolution mapping of measured molecular masses to peptides and proteins, irrespectively of the enzyme/digestion method used. Furthermore, multi-filtering may be applied in terms of measured mass tolerance, molecular mass and isoelectric point range as well as pattern matching to refine the results. This approach serves complementary to the existing solutions for protein identification and gives insights in novel peptides discovery and protein identification at the cases where the identification scores from the other approaches may be below significance threshold. Peptide Finder has been proven useful in proteomics procedures with experimental data from MALDI-TOF.

Availability: Peptide Finder web-application is available at http://bioserver-1.bioacademy.gr/Bioserver/PeptideFinder/.

Contact: gspyrou{at}bioacademy.gr

Associate Editor: Burkhard Rost

Received on April 18, 2008; revised on July 16, 2008; accepted on August 1, 2008

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A. Alexandridou, G. Th. Tsangaris, K. Vougas, K. Nikita, and G. Spyrou
UniMaP: finding unique mass and peptide signatures in the human proteome
Bioinformatics, November 15, 2009; 25(22): 3035 - 3037.
[Abstract] [Full Text] [PDF]


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