Research abstract
Letter abstract
Nature Biotechnology 25, 125 - 131 (2006)
Published online: 31 December 2006 | doi:10.1038/nbt1275
Computational prediction of proteotypic peptides for quantitative proteomics
Parag Mallick1,2,3, Markus Schirle4, Sharon S Chen3, Mark R Flory1, Hookeun Lee1,5, Daniel Martin1, Jeffrey Ranish1, Brian Raught1, Robert Schmitt4, Thilo Werner4, Bernhard Kuster4 & Ruedi Aebersold1
Mass spectrometry–based quantitative proteomics has become an important component of biological and clinical research. Although such analyses typically assume that a protein's peptide fragments are observed with equal likelihood, only a few so-called 'proteotypic' peptides are repeatedly and consistently identified for any given protein present in a mixture. Using >600,000 peptide identifications generated by four proteomic platforms, we empirically identified >16,000 proteotypic peptides for 4,030 distinct yeast proteins. Characteristic physicochemical properties of these peptides were used to develop a computational tool that can predict proteotypic peptides for any protein from any organism, for a given platform, with >85% cumulative accuracy. Possible applications of proteotypic peptides include validation of protein identifications, absolute quantification of proteins, annotation of coding sequences in genomes, and characterization of the physical principles governing key elements of mass spectrometric workflows (e.g., digestion, chromatography, ionization and fragmentation).
- Institute for Systems Biology, 1441 N. 34th Street, Seattle, Washington 98103, USA.
- Cedars-Sinai Medical Center, 8750 W. Beverly Blvd, Los Angeles, California 90048, USA.
- University of California, Los Angeles, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, USA.
- Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland.
Correspondence to: Ruedi Aebersold1 e-mail: rudolf.aebersold@imsb.biol.ethz.ch
Correspondence to: Bernhard Kuster4 e-mail: Bernhard.kuester@cellzome.com
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