SAMPI: protein identification with mass spectra alignments

Kaltenbach H-M, Wilke A, Böcker S (2007)
BMC Bioinformatics 8(1): 102.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
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.
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Zeitschriftentitel
BMC Bioinformatics
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8
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1
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102
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Kaltenbach H-M, Wilke A, Böcker S. SAMPI: protein identification with mass spectra alignments. BMC Bioinformatics. 2007;8(1):102.
Kaltenbach, H. - M., Wilke, A., & Böcker, S. (2007). SAMPI: protein identification with mass spectra alignments. BMC Bioinformatics, 8(1), 102. doi:10.1186/1471-2105-8-102
Kaltenbach, H. - M., Wilke, A., and Böcker, S. (2007). SAMPI: protein identification with mass spectra alignments. BMC Bioinformatics 8, 102.
Kaltenbach, H.-M., Wilke, A., & Böcker, S., 2007. SAMPI: protein identification with mass spectra alignments. BMC Bioinformatics, 8(1), p 102.
H.-M. Kaltenbach, A. Wilke, and S. Böcker, “SAMPI: protein identification with mass spectra alignments”, BMC Bioinformatics, vol. 8, 2007, pp. 102.
Kaltenbach, H.-M., Wilke, A., Böcker, S.: SAMPI: protein identification with mass spectra alignments. BMC Bioinformatics. 8, 102 (2007).
Kaltenbach, Hans-Michael, Wilke, Andreas, and Böcker, Sebastian. “SAMPI: protein identification with mass spectra alignments”. BMC Bioinformatics 8.1 (2007): 102.
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3 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

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PMID: 21247462
Feature-matching pattern-based support vector machines for robust peptide mass fingerprinting.
Li Y, Hao P, Zhang S, Li Y., Mol Cell Proteomics 10(12), 2011
PMID: 21775775

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