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.

AlgorithmNo. of proteins
1% FPR, 2 peptides1% FPR, 1 peptide5% FPR, 2 peptides5% FPR, 1 peptide95% PP, 2 peptides95% PP, 1 peptide90% PP, 2 peptides90% PP, 1 peptide
SEQUEST57711766311301574726632765
Mascot58711076361159578713630720
X!Tandem59612566481407585720641733