NAR Molecular Biology Database Collection entry number 950

http://www.mapuproteome.com

Zhang Y.^1,2, Zhang Y.^1,2, Adachi J.^1,3, Olsen J.V.¹, Shi R.¹, de Souza G.¹, Pasini E.⁴, Foster L.J.⁵, Macek B.¹, Zougman A.¹, Kumar C.¹, Wisniewski J.R.¹, Jun W.^2,6,7 and Mann M.¹

¹Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
²Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
³New address: Graduate School of Global Environmental Studi, Kyoto University, Yoshida-Honmachi Sakyo-Ku, Kyoto 606-8501, Japan
⁴Biomedical Primate Research Centre, Lange Kleiweg 139, 2288 GJ Rijswijk, The Netherlands
⁵ Centre for Proteomics, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
⁶Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark
⁷Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark

Contact mmann@biochem.mpg.de

Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) proteome database. MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3500 proteins. By employing high resolution MS and stringent validation criteria, false positive identification rates in MAPU are lower than 1:1000. Thus MAPU data sets can serve as reference proteomes in biomarker discovery. MAPU contains the peptides identifying each protein, measured masses, scores and intensities and is freely available at http://www.mapuproteome.com using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools.

We thank the database group at the Beijing Genome Institute for help, discussion and providing database templates.

Go to the abstract in the NAR 2007 Database Issue.

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