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Open Access Research article

SAMPI: Protein Identification with Mass Spectra Alignments

Hans-Michael Kaltenbach1*, Andreas Wilke2 and Sebastian Böcker3*

Author Affiliations

1 AG Genominformatik, Technische Fakultät, Universität Bielefeld, PF 100 131, 33501 Bielefeld, Germany

2 Computation Institute, University of Chicago, Chicago, IL 60637, USA

3 Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany

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BMC Bioinformatics 2007, 8:102  doi:10.1186/1471-2105-8-102

Published: 26 March 2007

Abstract

Background

Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database. However, existing tools for analyzing PMFs often suffer from missing or heuristic analysis of the significance of search results and insufficient handling of missing and additional peaks.

Results

We present an unified framework for analyzing Peptide Mass Fingerprints that offers a number of advantages over existing methods: First, comparison of mass spectra is based on a scoring function that can be custom-designed for certain applications and explicitly takes missing and additional peaks into account. The method is able to simulate almost every additive scoring scheme. Second, we present an efficient deterministic method for assessing the significance of a protein hit, independent of the underlying scoring function and sequence database. We prove the applicability of our approach using biological mass spectrometry data and compare our results to the standard software Mascot.

Conclusion

The proposed framework for analyzing Peptide Mass Fingerprints shows performance comparable to Mascot on small peak lists. Introducing more noise peaks, we are able to keep identification rates at a similar level by using the flexibility introduced by scoring schemes.