| Isolated rough and smooth microsomes of the endoplasmic reticulum and isolated Golgi apparatus from rat liver were analyzed by proteomics using mass spectrometry, identifying 1064 proteins among the three fractions. An additional 598 proteins were identified by biochemically subfractionating the rough and smooth microsomes by treatment with a high salt wash and the detergent Triton-X 114. Proteins were quantified by redundant peptide counts which enabled an assessment of the extent of cross-contamination between the endoplasmic reticulum and Golgi fractions and other organellar contamination. Results of this analysis revealed that the Golgi fraction was contaminated up to 30% by proteins of the endoplasmic reticulum and that the mitochondria constitute the largest source of organellar contamination for all three fractions. Hierarchical clustering of the distribution profiles of proteins among the three fractions assigned proteins to either the rough and/or smooth endoplasmic reticulum or the Golgi apparatus. In doing so, the protein disulphide isomerase, ERp44, was localized to the Golgi. This result was verified by immunolocalization with an ERp44 antibody. Furthermore, hierarchical clustering assigned a location for 176 previously uncharacterized proteins in the endoplasmic reticulum providing a subcellular context to their putative functions predicted by bioinformatics. Additionally, the biochemical subfractionation of the rough and smooth microsomes assigned proteins to the cytosolic, membrane or luminal subcompartments of the endoplasmic reticulum. These results guided the selection of uncharacterized membrane proteins for further characterization leading to the identification of 7 proteins upregulated by ER stress, which included 4 new molecular chaperones. Finally, a comparison of this work with previous proteomics analyses of these organelles showed that the proteomes of the endoplasmic reticulum and Golgi apparatus presented here may be the most comprehensive to date. The pipeline outlined in this thesis, which begins with well characterized and homogenous preparations of subcellular fractions, is documented as a comprehensive and quantitative approach to organellar proteomics. |
