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Table 3 Statistics for the current S. cerevisiae PeptideAtlas

From: Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

  Plimit = 0.9, Nobs > 0 Plimit = 0.95, Nobs > 0 Plimit = 0.99, Nobs > 0 Plimit = 0.9, Nobs > 1 Plimit = 0.95, Nobs > 1 Plimit = 0.99, Nobs > 1
# Experiments 47 47 47 47 47 47
# MS runs 2,579 2,579 2,579 2,579 2,579 2,579
# MS/MS 4.9 M 4.9 M 4.9 M 4.9 M 4.9 M 4.9 M
# MS/MS with P ≥ Plimit 600,960 565,217 472,234 586,708 552,434 461,827
# Distinct peptides with P ≥ Plimit 36,133 33,377 27,909 21,840 21,646 20,251
# Distinct peptides with perfect SGD alignment 35,434 32,790 27,499 21,469 21,281 19,942
# SGD ORFs seen in PeptideAtlas 4,249 (62%) 3,903 (57%) 3,476 (51%) 3,069 (45%) 3,049 (45%) 2,935 (43%)
# SGD ORFs unambiguously seen in PeptideAtlas 3,980 (59%) 3644 (54%) 3,224 (47%) 2,795 (41%) 2,778 (41%) 2,672 (39%)
  1. The percentage of SGD ORFs seen in PeptideAtlas is shown as a function of lower limit PeptideProphet probabilities and number of times peptide has been observed above lower limit. Using the most generous parameters of the build, we see 62% of the SGD ORFs. As an aside, 68% of SGD ORFs have Systematic gene names and we observe 76% of those. This is comparable to the 83% of ORFs with Systematic gene names that Ghaemmaghami et al. [14] observed in their protein expression study.