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Originally published In Press as doi:10.1074/mcp.M300073-MCP200 on December 26, 2003.
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Molecular & Cellular Proteomics 3:238-249, 2004.
© 2004 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

The Power and the Limitations of Cross-Species Protein Identification by Mass Spectrometry-driven Sequence Similarity Searches*,S

Bianca Habermann{ddagger},§,¶, Jeffrey Oegema§, Shamil Sunyaev|| and Andrej Shevchenko{ddagger},¶

From the {ddagger} Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; and || Birgham & Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115

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.

To whom correspondence should be addressed: Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. E-mail: habermann{at}mpi-cbg.de or shevchenko{at}mpi-cbg.de


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