000003031 001__ 3031 000003031 005__ 20251027121058.0 000003031 0247_ $$2DOI$$a10.6083/M4154G3H 000003031 037__ $$aETD 000003031 245__ $$aThe effects of parsimony logic and extended parsimony clustering on protein identification and quantification in shotgun proteomics 000003031 260__ $$bOregon Health and Science University 000003031 269__ $$a2016 000003031 336__ $$aThesis 000003031 502__ $$bM.S. 000003031 502__ $$gBioinformatics & Computational Biomedicine 000003031 520__ $$aShotgun proteomics is the most common mass spectrometry-based proteomics method for identifying and quantifying proteins present within a sample. Despite improvements in mass spectrometry tools, the issue dealing with inferring proteins and quantifying them from peptides still persists. The choice of protein sequence databases and the underlying genomic complexities of organisms are often considered sources of peptide degeneracy that lead to varying protein identifications and quantifications. In this thesis, the differences between four protein sequence database sources (Uniprot, NCBI, Ensembl, and IPI) were compared using redundant and non-redundant protein counts and shared and unique peptide counts for two higher eukaryotic organisms (human and mouse) and a representative lower eukaryotic organism (yeast). 000003031 540__ $$fCC BY 000003031 542__ $$fIn copyright - single owner 000003031 650__ $$aPeptides 000003031 650__ $$aDatabases, Protein$$033841 000003031 650__ $$aMass Spectrometry$$026224 000003031 650__ $$aProteomics$$035059 000003031 6531_ $$ascaffold-like clustering 000003031 6531_ $$aproteomic analysis workflow 000003031 6531_ $$aprotein sequence database 000003031 6531_ $$aquantitative information content 000003031 6531_ $$ashared peptides 000003031 6531_ $$ashotgun proteomics 000003031 691__ $$aSchool of Medicine$$041369 000003031 692__ $$aDepartment of Medical Informatics and Clinical Epidemiology$$041422 000003031 7001_ $$aMadhira, Raviteja$$uOregon Health and Science University$$041354$$10000-0001-6796-0522 000003031 7201_ $$aWilmarth, Phillip$$uOregon Health and Science University$$041354$$7Personal$$eMentor 000003031 7201_ $$aCohen, Aaron$$uOregon Health and Science University$$041354$$7Personal$$eAdvisor$$eMentor 000003031 8564_ $$916282f9a-841e-49a2-b4d7-04c2b3af83f4$$s1705966$$uhttps://digitalcollections.ohsu.edu/record/3031/files/3855_etd.pdf$$ePublic$$22eeeead36570f281fb1069326533cf5e$$31 000003031 905__ $$a/rest/prod/c5/34/fp/14/c534fp149 000003031 909CO $$ooai:digitalcollections.ohsu.edu:3031$$pstudent-work 000003031 980__ $$aTheses and Dissertations