Table 1.
Comparison of the performance of conventional criteria, PeptideProphet and SFOER in peptide identifications for the analysis of human liver tissue lysatea
| Conventional criteriab | PeptideProphetc | SFOERd | |
| # 1+ | 99 | 26 | 162 |
| # 2+ | 17950 | 17451 | 18606 |
| # 3+ | 7388 | 12587 | 11313 |
| # total | 25428 | 30064 | 30081 |
| %incr | / | 18.2% | 18.3% |
| # false pep | 126 | 113 | 147 |
| FDR | 0.99% | 0.75% | 0.98% |
| #unique pep | 4591 | 5175 | 5285 |
| %incr unique pep | / | 12.7% | 15.12% |
| # proteins | 1467 | 1596 | 1665 |
a. Summary of each category returned by different strategies: #1+, #2+ and #3+ indicates the number of peptide identifications for charge states of 1+, 2+ and 3+ respectively. #total = (#1+) + (#2+) + (#3+). #false pep indicates the number of peptides from reversed database, while #unique pep is the number of total unique peptides. Increase of peptide identifications (%incr) and unique peptide identifications (%incr unique pep) by SFOER and PeptideProphet are shown. #proteins are the number of positive proteins identified by the strategies. FDR of identifications are also shown.
b. Conventional criteria. Xcorr > 2.0, 2.5 and 3.8 for singly, doubly and triply charged peptides, respectively and ΔCn > 0.164 for all charge states [25, 33].
c. Cutoff is set as PeptideProphet probability > 0.9 [13, 36-38].
d. Optimized criteria determined by SFOER are: according to the charge states of 1+, 2+ and 3+, Xcorr scores > 1.76, 2.31 and 2.41, ΔCn > 0.061, 0.199 and 0.265, Sp > 44.42, 104 and 276.9 and Rsp < 3, 4 and 2.