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DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets.

TitleDtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets.
Publication TypeJournal Article
Year of Publication2010
AuthorsPetyuk VA, Mayampurath AM, Monroe ME, Polpitiya AD, Purvine SO, Anderson GA, Camp DG, Smith RD
JournalMol Cell Proteomics
KeywordsAlgorithms, Amino Acid Sequence, Automatic Data Processing, Databases, Protein, Peptides, Proteomics, Software Design, Tandem Mass Spectrometry
Abstract

Hybrid two-stage mass spectrometers capable of both highly accurate mass measurement and high throughput MS/MS fragmentation have become widely available in recent years, allowing for significantly better discrimination between true and false MS/MS peptide identifications by the application of a relatively narrow window for maximum allowable deviations of measured parent ion masses. To fully gain the advantage of highly accurate parent ion mass measurements, it is important to limit systematic mass measurement errors. Based on our previous studies of systematic biases in mass measurement errors, here, we have designed an algorithm and software tool that eliminates the systematic errors from the peptide ion masses in MS/MS data. We demonstrate that the elimination of the systematic mass measurement errors allows for the use of tighter criteria on the deviation of measured mass from theoretical monoisotopic peptide mass, resulting in a reduction of both false discovery and false negative rates of peptide identification. A software implementation of this algorithm called DtaRefinery reads a set of fragmentation spectra, searches for MS/MS peptide identifications using a FASTA file containing expected protein sequences, fits a regression model that can estimate systematic errors, and then corrects the parent ion mass entries by removing the estimated systematic error components. The output is a new file with fragmentation spectra with updated parent ion masses. The software is freely available.

DOI10.1074/mcp.M900217-MCP200
PubMed ID20019053
PubMed Central IDPMC2849711
Grant ListP41 RR018522-07 / RR / NCRR NIH HHS / United States
RR18522 / RR / NCRR NIH HHS / United States
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