Abstract
DESPITE THE INCREASING popularity of mass spectrometry for both discovery-driven and quantitative proteomics, doubts have persisted about the reproducibility of the measurements. Those doubts must be put to rest before such methods will be widely accepted for identification, verification, and validation of protein biomarkers of disease. Two recent multilaboratory studies suggest that the outlook for mass spectrometry-based proteomics is promising, although trouble spots remain. In the first study, sponsored by the Human Proteome Organization (HUPO), 24 academic and three vendor laboratories analyzed a sample consisting of 20 human proteins by mass spectrometry ( Nat.Methods 2009, 6, 423). Each protein contained at least one unique 1,250-dalton peptide, and participants were asked to analyze these peptides as well. Other than providing the participants a database to search, the organizers gave the participants free rein to carry out the analysis, says lead author John J.M. Bergeron of McGill University, in...
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