Table II.
Comparison of number of proteins identified by each search algorithm with decoy database FPR calculations and PeptideProphet and ProteinProphet probability calculations for both a minimum of one and two peptides per protein
For each FPR, all protein identifications were filtered by algorithm-specific peptide threshold cutoffs: SEQUEST: Xcorr and ΔCn; Mascot: identity and ion scores; and X!Tandem: log(e) value. PP, PeptideProphet & ProteinProphet probability.
| Algorithm | No. of proteins
|
|||||||
|---|---|---|---|---|---|---|---|---|
| 1% FPR, 2 peptides | 1% FPR, 1 peptide | 5% FPR, 2 peptides | 5% FPR, 1 peptide | 95% PP, 2 peptides | 95% PP, 1 peptide | 90% PP, 2 peptides | 90% PP, 1 peptide | |
| SEQUEST | 577 | 1176 | 631 | 1301 | 574 | 726 | 632 | 765 |
| Mascot | 587 | 1107 | 636 | 1159 | 578 | 713 | 630 | 720 |
| X!Tandem | 596 | 1256 | 648 | 1407 | 585 | 720 | 641 | 733 |