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dc.contributor.authorLakbub, Jude C.
dc.contributor.authorSu, Xiaomeng
dc.contributor.authorZhu, Zhikai
dc.contributor.authorPatabandige, Milani W.
dc.contributor.authorHua, David
dc.contributor.authorGo, Eden P.
dc.contributor.authorDesaire, Heather
dc.identifier.citationLakbub, J. C., Su, X., Zhu, Z., Patabandige, M. W., Hua, D., Go, E. P., & Desaire, H. (2017). Two New Tools for Glycopeptide Analysis Researchers: A Glycopeptide Decoy Generator and a Large Data Set of Assigned CID Spectra of Glycopeptides. Journal of proteome research, 16(8), 3002–3008. doi:10.1021/acs.jproteome.7b00289en_US
dc.descriptionThis document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Proteome Research, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see, see
dc.description.abstractThe glycopeptide analysis field is tightly constrained by a lack of effective tools that translate mass spectrometry data into meaningful chemical information, and perhaps the most challenging aspect of building effective glycopeptide analysis software is designing an accurate scoring algorithm for MS/MS data. We provide the glycoproteomics community with two tools to address this challenge. The first tool, a curated set of 100 expert-assigned CID spectra of glycopeptides, contains a diverse set of spectra from a variety of glycan types; the second tool, Glycopeptide Decoy Generator, is a new software application that generates glycopeptide decoys de novo. We developed these tools so that emerging methods of assigning glycopeptides’ CID spectra could be rigorously tested. Software developers or those interested in developing skills in expert (manual) analysis can use these tools to facilitate their work. We demonstrate the tools’ utility in assessing the quality of one particular glycopeptide software package, GlycoPep Grader, which assigns glycopeptides to CID spectra. We first acquired the set of 100 expert assigned CID spectra; then, we used the Decoy Generator (described herein) to generate 20 decoys per target glycopeptide. The assigned spectra and decoys were used to test the accuracy of GlycoPep Grader’s scoring algorithm; new strengths and weaknesses were identified in the algorithm using this approach. Both newly developed tools are freely available. The software can be downloaded at
dc.publisherAmerican Chemical Societyen_US
dc.rights© 2017 American Chemical Societyen_US
dc.subjectFalse Discovery Rateen_US
dc.subjectCollision Induced Dissociationen_US
dc.subjectLiquid Chromatography-Mass Spectrometryen_US
dc.titleTwo New Tools for Glycopeptide Analysis Researchers: A Glycopeptide Decoy Generator and a Large Data Set of Assigned CID Spectra of Glycopeptidesen_US
kusw.kuauthorLakbub, Jude C.
kusw.kuauthorSu, Xiaomeng
kusw.kuauthorZhu, Zhikai
kusw.kuauthorPatabandige, Milani W.
kusw.kuauthorHua, David
kusw.kuauthorGo, Eden P.
kusw.kuauthorDesaire, Heather
kusw.kudepartmentDepartment of Chemistryen_US
kusw.oaversionScholarly/refereed, author accepted manuscripten_US
kusw.oapolicyThis item meets KU Open Access policy criteria.en_US

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