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Originally published In Press as doi:10.1074/mcp.M300022-MCP200 on June 9, 2003.
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Molecular & Cellular Proteomics 2:405-414, 2003.
© 2003 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Affinity Proteomics for Systematic Protein Profiling of Chromosome 21 Gene Products in Human Tissues*

Charlotta Agaton{ddagger}, Joakim Galli§, Ingmarie Höidén Guthenberg§, Lars Janzon§, Marianne Hansson§, Anna Asplund, Eva Brundell§, Susanne Lindberg§, Irene Ruthberg§, Kenneth Wester, Dorothee Wurtz§, Christer Höög|, Joakim Lundeberg{ddagger}, Stefan Ståhl{ddagger}, Fredrik Pontén and Mathias Uhlén{ddagger},**

From the {ddagger} Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Roslagsvägen 30 B, 106 91 Stockholm, Sweden, § Affibody AB, Box 20137, 161 02 Stockholm, Sweden, Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden, and | Center for Genomics and Bioinformatics, Karolinska Institute, Berzelius väg 35, 171 77 Stockholm, Sweden

Here we show that an affinity proteomics strategy using affinity-purified antibodies raised against recombinant human protein fragments can be used for chromosome-wide protein profiling. The approach is based on affinity reagents raised toward bioinformatics-designed protein epitope signature tags corresponding to unique regions of individual gene loci. The genes of human chromosome 21 identified by the genome efforts were investigated, and the success rates for de novo cloning, protein production, and antibody generation were 85, 76, and 56%, respectively. Using human tissue arrays, a systematic profiling of protein expression and subcellular localization was undertaken for the putative gene products. The results suggest that this affinity proteomics strategy can be used to produce a proteome atlas, describing distribution and expression of proteins in normal tissues as well as in common cancers and other forms of diseased tissues.

** To whom correspondence should be addressed: Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Roslagsvägen 30 B, 106 91 Stockholm, Sweden. Tel.: +46855378325; Fax: +46855378482; E-mail: mathias.uhlen{at}biotech.kth.se


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