Table 4

Expected errors

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%)


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.

King et al. Genome Biology 2006 7:R106   doi:10.1186/gb-2006-7-11-r106

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