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Table 4 Expected errors

From: Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

Case Expected errors Plimit = 0.9 Expected errors Plimit = 0.95 Expected errors Plimit = 0.99
MS/MS Pi ≥ Plimit 0.00915 (9%) 0.00517 (5%) 0.00137 (1%)
MS/MS Pi ≥ Plimit, Npeptide observed > 1 0.00884 (9%) 0.00506 (5%) 0.00136 (1%)
Consensus peptide best Pi, Pi ≥ Plimit 0.01027 (10%) 0.00510 (5%) 0.00120 (1%)
Consensus peptide best Pi, Pi ≥ Plimit, Npeptide observed >1 0.00272 (3%) 0.00215 (2%) 0.00078 (1%)
  1. Expected errors in the Saccharomyces PeptideAtlas are calculated for four cases and lower probability limits (Plimit = 0.9, 0.95, 0.99): the assigned probability P of each MS/MS is used for all Pi ≥ Plimit; the assigned probability P of each MS/MS is used for all Pi ≥ Plimit where the associated peptide has been seen in the S. cerevisiae PeptideAtlas more than once'; the best probability for each unique peptide sequence is used for all Pi ≥ Plimit; the best probability for each unique peptide sequence is used for all Pi ≥ Plimit when the peptide has been seen in the S. cerevisiae PeptideAtlas more than once.