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Submitted on January 24, 2007
Revised on May 4, 2007
Accepted on May 28, 2007

The Implications of Proteolytic Background for Shotgun Proteomics

Paola Picotti, Ruedi Aebersold, and Bruno Domon

IMSB, Institute of Molecular Systems Biology, ETH Zuerich, Zuerich CH-8093

Corresponding Author: domon{at}imsb.biol.ethz.ch

The analysis by liquid chromatography coupled to tandem mass spectrometry of complex peptide mixtures, generated by proteolysis of protein samples, is the main proteomic method used today. The approach is based on the assumption that each protein present in a sample reproducibly and predictably generates a relatively small number of peptides that can be identified by mass spectrometry. In this study this assumption was examined by a targeted peptide sequencing strategy, using inclusion lists to trigger peptide fragmentation attempts. It was found that the number of peptides observed from a single protein is at least one order of magnitude greater than previously assumed. This unexpected complexity of proteomic samples implies substantial technical challenges, explains some perplexing results in the proteomic literature, and prompts the need for developing alternative experimental strategies for the rapid and comprehensive analysis of proteomes.


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