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Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases

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dc.contributor.author Barsnes, Harald
dc.contributor.author Mikalsen, Svein-Ole
dc.contributor.author Eidhammer, Ingvar
dc.date.accessioned 2010-08-10T08:34:41Z
dc.date.available 2010-08-10T08:34:41Z
dc.date.issued 2008-12-19
dc.identifier.citation BMC Research Notes 1(130) en
dc.identifier.issn 1756-0500
dc.identifier.uri http://dx.doi.org/10.1186/1756-0500-1-130
dc.identifier.uri http://hdl.handle.net/1956/4015
dc.description.abstract Background: Mass spectrometric analysis of peptides is an essential part of protein identification and characterization, the latter meaning the identification of modifications and amino acid substitutions. There are two main approaches for characterization: (i) using a predefined set of possible modifications and substitutions or (ii) performing a blind search. The first option is straightforward, but can not detect modifications or substitutions outside the predefined set. A blind search does not have this limitation, and therefore has the potential of detecting both known and unknown modifications and substitutions. Combining the peptide mass fingerprints from two proteases result in overlapping sequence coverage of the protein, thereby offering alternative views of the protein and a novel way of indicating post-translational modifications and amino acid substitutions. Results: We have developed an algorithm and a software tool, MassShiftFinder, that performs a blind search using peptide mass fingerprints from two proteases with different cleavage specificities. The algorithm is based on equal mass shifts for overlapping peptides from the two proteases used, and can indicate both post-translational modifications and amino acid substitutions. In most cases it is possible to suggest a restricted area within the overlapping peptides where the mass shift can occur. The program is available at http://www.bioinfo.no/software/massShiftFinder. Conclusion: Without any prior assumptions on their presence the described algorithm is able to indicate post-translational modifications or amino acid substitutions in MALDI-TOF experiments on identified proteins, and can thereby direct the involved peptides to subsequent TOF-TOF analysis. The algorithm is designed for detailed and low-throughput characterization of single proteins. en
dc.language.iso eng en
dc.publisher BioMed Central en
dc.rights Copyright 2008 Barsnes et al; licensee BioMed Central en
dc.rights.uri http://creativecommons.org/licenses/by/2.0/
dc.title Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases en
dc.type Journal article en
dc.type Peer reviewed en
dc.subject.nsi VDP::Teknologi: 500::Informasjons- og kommunikasjonsteknologi: 550 no
dc.rightsHolder Barsnes et al


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Copyright 2008 Barsnes et al; licensee BioMed Central Except where otherwise noted, this item's license is described as Copyright 2008 Barsnes et al; licensee BioMed Central

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