DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring

@article{citeulike:3032905, abstract = {Abstract: In shotgun proteomics, tandem mass spectra of peptides are typically identified through database search algorithms such as Sequest. We have developed DirecTag, an open-source algorithm to infer partial sequence tags directly from observed fragment ions. This algorithm is unique in its implementation of three separate scoring systems to evaluate each tag on the basis of peak intensity, m/z fidelity, and complementarity. In data sets from several types of mass spectrometers, DirecTag reproducibly exceeded the accuracy and speed of InsPecT and GutenTag, two previously published algorithms for this purpose. The source code and binaries for DirecTag are available from http://fenchurch.mc.vanderbilt.edu.}, address = {Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8575, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8340, Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0146, Institute for Systems Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98103}, author = {Tabb, David L. and Ma, Ze-Qiang and Martin, Daniel B. and Ham, Amy-Joan L. and Chambers, Matthew C. }, citeulike-article-id = {3032905}, doi = {10.1021/pr800154p}, journal = {J. Proteome Res.}, keywords = {bioinformatics, proteomics}, month = {July}, posted-at = {2008-07-22 15:38:33}, priority = {2}, title = {DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring}, url = {http://dx.doi.org/10.1021/pr800154p}, year = {2008} }

TY - JOUR ID - citeulike:3032905 L3 - citeulike-article-id:3032905 TI - DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring JF - J. Proteome Res. AD - Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8575, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8340, Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0146, Institute for Systems Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98103 N2 - Abstract: In shotgun proteomics, tandem mass spectra of peptides are typically identified through database search algorithms such as Sequest. We have developed DirecTag, an open-source algorithm to infer partial sequence tags directly from observed fragment ions. This algorithm is unique in its implementation of three separate scoring systems to evaluate each tag on the basis of peak intensity, m/z fidelity, and complementarity. In data sets from several types of mass spectrometers, DirecTag reproducibly exceeded the accuracy and speed of InsPecT and GutenTag, two previously published algorithms for this purpose. The source code and binaries for DirecTag are available from http://fenchurch.mc.vanderbilt.edu. KW - bioinformatics KW - proteomics AU - Tabb, David AU - Ma, Ze-Qiang AU - Martin, Daniel AU - Ham, Amy-Joan AU - Chambers, Matthew PY - 2008/07/17/ UR - http://dx.doi.org/10.1021/pr800154p ER -