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A more recent version of this article appeared on March 1, 2004.
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Submitted on July 31, 2003
Revised on December 22, 2003
Accepted on December 26, 2003

The power and the limitations of cross-species protein identification by mass spectrometry driven sequence similarity searches

Bianca Habermann, Jeffrey Oegema, Shamil Sunyaev, and Andrej Shevchenko

Department of Molecular Cell Biology and Genetics, MPI, Dresden, Dresden 01307

Corresponding Author: shevchenko{at}mpi-cbg.de

Mass spectrometry driven BLAST (MS BLAST) is a database search protocol for identifying unknown proteins by sequence similarity to homologous proteins available in a database. MS BLAST utilizes redundant, degenerate and partially inaccurate peptide sequence data, obtained by de novo interpretation of tandem mass spectra and has become a powerful tool in functional proteomic research. Using computational modeling we evaluated the potential of MS BLAST for proteome-wide identification of unknown proteins. We determined how the success rate of protein identification depends on the full-length sequence identity between the queried protein and its closest homologue in a database. We also estimated phylogenetic distances between organisms under study and related reference organisms with completely sequenced genomes that allow substantial coverage of unknown proteomes.


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