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Submitted on July 1, 2004
Research Center for Proteome Analysis, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031
Corresponding Author: zr{at}sibs.ac.cn
Subcellular proteomics, as an important step to functional proteomics, has been a focus in proteomic research. However, the co-purification of ‘contaminating’ proteins has been the major problem in all the subcellular proteomic research including all kinds of mitochondrial proteome research. It is often difficult to conclude whether these ‘contaminants’ represent true endogenous partners or artificial associations induced by cell disruption or incomplete purification. To solve such a problem, we applied a high-throughput comparative proteome experimental strategy, isotope-coded affinity tag (ICAT) approach performed with two-dimensional liquid chromatography tandem mass spectrometry analysis, coupled with combinational usage of different bioinformatics tools, to study the proteome of rat liver mitochondria prepared with traditional centrifugation (CM) or further purified with a Nycodenz gradient (PM). A total of 169 proteins were identified and quantified convincingly in the ICAT analysis, in which, 90 proteins have ICAT ratio of PM:CM >1.0 while another 79 proteins have ICAT ratio of PM:CM <1.0. Almost all the proteins annotated as mitochondrial according to Swiss-Prot annotation, bioinformatics prediction and literature reports have the ratio of PM:CM >1.0, while proteins annotated as extracellular or secreted, cytoplasmic, endoplasmic reticulum, ribosomal and so on, have ratio of PM:CM <1.0. Catalase and AP endonuclease 1, which have been known as peroxisomal and nuclear respectively, have shown ratio of PM:CM >1.0, confirming the reports about their mitochondrial location.
Revised on October 18, 2004
Accepted on October 25, 2004
A Comparative Proteomic Strategy for Subcellular Proteome Research : Isotope-coded Affinity Tag Approach Coupled with Bioinformatics Prediction to Ascertain Rat Liver Mitochondrial Proteins and Indication of Mitochondrial Localization for Catalase
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