SAMPI: Protein Identification with Mass Spectra Alignments

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 functi...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Hans-Michael Kaltenbach, Andreas Wilke, Sebastian Böcker
• Keywords: BMCBI 2007, Mass, Peptide Mass, Protein