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dc.contributor.advisorMacCoss, Michael Jen_US
dc.contributor.authorFinney, Gregory L.en_US
dc.date.accessioned2012-08-10T20:25:50Z
dc.date.available2012-08-10T20:25:50Z
dc.date.issued2012-08-10
dc.date.submitted2012en_US
dc.identifier.otherFinney_washington_0250E_10114.pdfen_US
dc.identifier.urihttp://hdl.handle.net/1773/20263
dc.descriptionThesis (Ph.D.)--University of Washington, 2012en_US
dc.description.abstractThe comparative measurement of protein abundance is a powerful method to detect changes in the biological dynamics of cells and tissues. Shotgun proteomics has proven to be a method where a wide range of proteins can be characterized in a single experiment by analysis of their peptide digests using micro-capillary liquid chromatography coupled to mass spectrometry (μLC-MS). We have the CRAWDAD software tool for label-free relative quantitation between samples using peptide signals in μLC-MS data associated with their identifications from MS/MS data. CRAWDAD discovers features for quantification in μLC-MS data, lowers chromatographic and signal variance across replicates, and finds statistically significant changes in peptide abundance between samples. We have applied this tool toward model systems of induced expression of the <italic>Lac</italic> operator in <italic>E. coli</italic> to qualitatively assess the protein changes detected. A controlled set of changes using an <italic>E. coli</italic> protein digest spiked in at changing levels over a constant background of human proteins assesses the precision and accuracy of the detected changes in peptide and protein levels, and showed our results to be superior to label-free quantitation using spectral counting.en_US
dc.format.mimetypeapplication/pdfen_US
dc.language.isoen_USen_US
dc.rightsCopyright is held by the individual authors.en_US
dc.subjectBioinformatics; Genomics; Label-Free; Mass Spectrometry; Proteomics; Retention Time Alignmenten_US
dc.subject.otherBioinformaticsen_US
dc.subject.otherBiochemistryen_US
dc.subject.otherAnalytical chemistryen_US
dc.subject.otherGeneticsen_US
dc.titleTools and Analyses for Differential Label-Free Proteomics Using Mass Spectrometryen_US
dc.typeThesisen_US
dc.embargo.termsNo embargoen_US


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