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Submitted on November 20, 2002
Revised on January 27, 2003
Accepted on February 10, 2003
Banting & Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6
Corresponding Author: andrew.emili{at}utoronto.ca
We have developed a systematic analytical approach, termed PRISM, which permits routine, large-scale protein expression profiling of mammalian cells and tissues. PRISM combines subcellular fractionation, multidimensional liquid chromatography-tandem mass spectrometry-based protein shotgun sequencing, and two newly developed computer algorithms, STATQUEST and GOClust, as a means to rapidly identify, annotate and categorize thousands of expressed mammalian proteins. The application of PRISM to adult mouse lung and liver resulted in the high-confidence identification of over 2,100 unique proteins, including more than 100 integral membrane proteins, 400 nuclear proteins and 500 uncharacterized proteins - the largest proteome study carried out to date on this important model organism. Automated clustering of the identified proteins into GO annotation groups allowed for streamlined analysis of the large dataset, revealing physiologically relevant patterns of tissue and organelle specificity. PRISM therefore offers an effective platform for in-depth investigation of complex mammalian proteomes.
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