PhosphoScore: An Open-Source Phosphorylation Site Assignment Tool for MSn Data

@article{citeulike:2882583, abstract = {Abstract: Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To this end, we have created PhosphoScore, an open-source assignment program that is compatible with phosphopeptide data from multiple MS levels (MSn). The algorithm takes into account both the match quality and normalized intensity of observed spectral peaks compared to a theoretical spectrum. PhosphoScore produced >95\% correct MS2 assignments from known synthetic data, > 98\% agreement with an established MS2 assignment algorithm (Ascore), and >92\% agreement with visual inspection of MS3 and MS4 spectra.}, address = {Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892}, author = {Ruttenberg, Brian E. and Pisitkun, Trairak and Knepper, Mark A. and Hoffert, Jason D. }, citeulike-article-id = {2882583}, doi = {http://dx.doi.org/10.1021/pr800169k}, journal = {J. Proteome Res.}, keywords = {analysis, mass-spec, opensource, phosphorylation, software}, month = {June}, posted-at = {2008-06-11 13:05:16}, priority = {2}, title = {PhosphoScore: An Open-Source Phosphorylation Site Assignment Tool for MSn Data}, url = {http://dx.doi.org/10.1021/pr800169k}, year = {2008} }

TY - JOUR ID - citeulike:2882583 L3 - citeulike-article-id:2882583 N2 - Abstract: Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To this end, we have created PhosphoScore, an open-source assignment program that is compatible with phosphopeptide data from multiple MS levels (MSn). The algorithm takes into account both the match quality and normalized intensity of observed spectral peaks compared to a theoretical spectrum. PhosphoScore produced >95% correct MS2 assignments from known synthetic data, > 98% agreement with an established MS2 assignment algorithm (Ascore), and >92% agreement with visual inspection of MS3 and MS4 spectra. JF - J. Proteome Res. AD - Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892 TI - PhosphoScore: An Open-Source Phosphorylation Site Assignment Tool for MSn Data KW - analysis KW - mass-spec KW - opensource KW - phosphorylation KW - software AU - Ruttenberg, Brian AU - Pisitkun, Trairak AU - Knepper, Mark AU - Hoffert, Jason PY - 2008/06/11/ UR - http://dx.doi.org/10.1021/pr800169k ER -