TY  - THES
AB  - Shotgun 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).
AD  - Oregon Health and Science University
AU  - Madhira, Raviteja
DA  - 2016
DO  - 10.6083/M4154G3H
DO  - DOI
ED  - Wilmarth, Phillip
ED  - Cohen, Aaron
ED  - Mentor
ED  - Advisor
ED  - Mentor
ID  - 3031
KW  - Peptides
KW  - Databases, Protein
KW  - Mass Spectrometry
KW  - Proteomics
KW  - scaffold-like clustering
KW  - proteomic analysis workflow
KW  - protein sequence database
KW  - quantitative information content
KW  - shared peptides
KW  - shotgun proteomics
L1  - https://digitalcollections.ohsu.edu/record/3031/files/3855_etd.pdf
L2  - https://digitalcollections.ohsu.edu/record/3031/files/3855_etd.pdf
L4  - https://digitalcollections.ohsu.edu/record/3031/files/3855_etd.pdf
LK  - https://digitalcollections.ohsu.edu/record/3031/files/3855_etd.pdf
N2  - Shotgun 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).
PB  - Oregon Health and Science University
PY  - 2016
T1  - The effects of parsimony logic and extended parsimony clustering on protein identification and quantification in shotgun proteomics
TI  - The effects of parsimony logic and extended parsimony clustering on protein identification and quantification in shotgun proteomics
UR  - https://digitalcollections.ohsu.edu/record/3031/files/3855_etd.pdf
Y1  - 2016
ER  -