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.

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