Journal
JOURNAL OF PROTEOME RESEARCH
Volume 8, Issue 9, Pages 4173-4181Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr9004794
Keywords
two-peptide rule; false discovery rate; mass spectrometry; peptide identification; protein identification; decoy database; false positives
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Funding
- NIH [5R01RR016522-05, 1-P41-RR024851-01]
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Most proteomics studies attempt to maximize the number of peptide identifications and subsequently infer proteins containing two or more peptides as reliable protein identifications. In this study, we evaluate the effect of this two-peptide rule on protein identifications, using multiple search tools and data sets. Contrary to the intuition, the two-peptide rule reduces the number of protein identifications in the target database more significantly than in the decoy database and results in increased false discovery rates, compared to the case when single-hit proteins are not discarded. We therefore recommend that the two-peptide rule should be abandoned, and instead, protein identifications should be subject to the estimation of error rates, as is the case with peptide identifications. We further extend the generating function approach (originally proposed for evaluating matches between a peptide and a single spectrum) to evaluating matches between a protein and an entire spectral data set.
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