Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

Table 5 Numbers of proteins matching SGD ORF annotation categories

ORF annotation	SGD	PeptideAtlas P > 0.9, N_obs > 0	PeptideAtlas P > 0.9, N_obs > 1
Uncharacterized	1,414	695 (49%)	405 (29%)
Verified	4,366	3,250 (74%)	2,449 (56%)
Verified \| silenced gene	4	1 (25%)	0 (0%)
Dubious	820	95 (12%)	13 (2%)
Pseudogene	21	4 (19%)	1 (5%)
Transposable element gene	89	18 (20%)	13 (15%)
Total	6,714	4,063 (61%)	2,881 (43%)

The percent of SGD ORFs seen in the PeptideAtlas are shown in columns 3 and 4. Column 3 uses all peptides with probabilities ≥ 0.9, while column 4 excludes peptides that have only been seen once in the S. cerevisiae PeptideAtlas.

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