Table I

Number of MS/MS spectra, confident peptide identifications, and inferred protein identification from analyzing a fraction of yeast proteome digest using three different data-dependent MS/MS acquisition strategies in 90-min LC-MS/MS analyses (mean and S.D. from three analyses)

Peptide and protein identification false-positive rates are given in parentheses. IDs, identifications.

LTQ10FT10SIM3
Acquired MS/MS spectra17,627 ± 57314,701 ± 1075,920 ± 37
Peptide IDs3,663 ± 29 (0.9 ± 0.3%)4,034 ± 36 (1.0 ± 0.1%)2,705 ± 28 (1.0 ± 0.3%)
Protein IDs394 ± 7 (9 ± 3%)397 ± 5 (9 ± 0%)236 ± 6 (10 ± 3%)