Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

Table 3 Statistics for the current S. cerevisiae PeptideAtlas

	P_limit = 0.9, N_obs > 0	P_limit = 0.95, N_obs > 0	P_limit = 0.99, N_obs > 0	P_limit = 0.9, N_obs > 1	P_limit = 0.95, N_obs > 1	P_limit = 0.99, N_obs > 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 ≥ P_limit	600,960	565,217	472,234	586,708	552,434	461,827
# Distinct peptides with P ≥ P_limit	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%)

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.

ISSN: 1474-760X