Publications:Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting

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Title Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting
Author Jim Samuelsson and Daniel Dalevi and Fredrik Levander and Thorsteinn Rögnvaldsson
Year 2004
PublicationType Journal Paper
Journal Bioinformatics
HostPublication
Conference
DOI http://dx.doi.org/10.1093/bioinformatics/bth460
Diva url http://hh.diva-portal.org/smash/record.jsf?searchId=1&pid=diva2:237422
Abstract A set of new algorithms and software tools for automatic protein identification using peptide mass fingerprinting is presented. The software is automatic, fast and modular to suit different laboratory needs, and it can be operated either via a Java user interface or called from within scripts. The software modules do peak extraction, peak filtering and protein database matching, and communicate via XML. Individual modules can therefore easily be replaced with other software if desired, and all intermediate results are available to the user. The algorithms are designed to operate without human intervention and contain several novel approaches. The performance and capabilities of the software is illustrated on spectra from different mass spectrometer manufacturers, and the factors influencing successful identification are discussed and quantified.