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Tools and Analyses for Differential Label-Free Proteomics Using Mass Spectrometry

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dc.contributor.advisor MacCoss, Michael J en_US Finney, Gregory L. en_US 2012-08-10T20:25:50Z 2012-08-10T20:25:50Z 2012-08-10 2012 en_US
dc.identifier.other Finney_washington_0250E_10114.pdf en_US
dc.description Thesis (Ph.D.)--University of Washington, 2012 en_US
dc.description.abstract The 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.mimetype application/pdf en_US
dc.language.iso en_US en_US
dc.rights Copyright is held by the individual authors. en_US
dc.subject Bioinformatics; Genomics; Label-Free; Mass Spectrometry; Proteomics; Retention Time Alignment en_US
dc.subject.other Bioinformatics en_US
dc.subject.other Biochemistry en_US
dc.subject.other Analytical chemistry en_US
dc.subject.other Genetics en_US
dc.title Tools and Analyses for Differential Label-Free Proteomics Using Mass Spectrometry en_US
dc.type Thesis en_US
dc.embargo.terms No embargo en_US

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