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Originally published In Press as doi:10.1074/mcp.M200074-MCP200 on February 10, 2003.
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Molecular & Cellular Proteomics 2:96-106, 2003.
© 2003 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

PRISM, a Generic Large Scale Proteomic Investigation Strategy for Mammals*,S

Thomas Kislinger{ddagger},§,¶, Khaled Rahman{ddagger},§,||, Dragan Radulovic§,**, Brian Cox§,{ddagger}{ddagger}, Janet Rossant{ddagger}{ddagger} and Andrew Emili{ddagger},§§

{ddagger} Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
** Department of Statistics, Yale University, New Haven, Connecticut 06520
{ddagger}{ddagger} Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada

We have developed a systematic analytical approach, termed PRISM (Proteomic Investigation Strategy for Mammals), that 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 Gene Ontology annotation groups allowed for streamlined analysis of the large data set, revealing interesting and 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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  		TABLE I Numerical summary of the proteins (peptides) detected by PRISM in mouse lung and liver tissue

The total number of high confidence peptides and corresponding proteins that pass the STATQUEST p value <0.02 filter cut-off are as follows: total peptides, 24,305; unique peptides, 8,606; unique proteins, 2,106. A summary of the protein distributions detected in the lung and liver fractions are shown. N, nucleus; C, cytosol; MS, soluble mitochondria; MP, insoluble mitochondria; MI, microsomes.

 

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  		TABLE II Summary of the cytochrome P450 isoforms detected in the microsomal membrane fractions of lung and liver

 
§§ To whom correspondence should be addressed: CH Best Inst., 112 College St., Rm. 402, Toronto, Ontario M5G 1L6, Canada. Tel.: 416-946-7281; Fax: 416-978-8528; Email: andrew.emili{at}utoronto.ca




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