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Algorithms for shotgun proteomics spectral identification and quality assessment

dc.creatorMa, Zeqiang
dc.description.abstractTandem mass spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. Assessing the full information content of shotgun proteomics experiments has motivated a series of powerful bioinformatics advances. Here I present three bioinformatics tools for shotgun proteomics spectral identification and quality assessment. The IDBoost tool is a post-identification analysis tool that rescues spectral identifications and corrects identification errors by incorporating the relationships inferred through spectral clustering. The ScanRanker tool offers a way to recover unidentified high quality spectra for additional analysis via the assessment of tandem mass spectral quality. The QuaMeter tool focuses on the quality assessment of shotgun proteomics experiments and provides objective criteria for the evaluation of analytical system variability. Each tool was developed to solve one aspect of problems but together they work coordinately to provide an improved shotgun proteomics data analysis pipeline. The source code and binaries of these tools are available from
dc.subjectmass spectrometry
dc.subjectquality assessment
dc.subjectquality control
dc.subjectpeptide identification
dc.titleAlgorithms for shotgun proteomics spectral identification and quality assessment
dc.contributor.committeeMemberDaniel C. Liebler
dc.contributor.committeeMemberBing Zhang
dc.contributor.committeeMemberKathleen L. Gould
dc.contributor.committeeMemberZhongming Zhao
dc.type.materialtext Informatics University
dc.contributor.committeeChairDavid L. Tabb

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