Table II

Comparison of MS2 and distinct peptide hits per protein by algorithm at various thresholds

Algorithm: thresholdMS2 hits per proteinDistinct peptide hits per protein
Mascot: identity14.14.9
Mascot: identity and homology14.14.9
Mascot: expectation, 1% MS2 FDR14.75.0
OMSSA: expectation, 1% MS2 FDR17.75.0
X! Tandem: expectation, 1% MS2 FDR15.05.2
Sequest: probability, 1% MS2 FDR13.24.7
Sequest: HUPO high12.74.1
Sequest: HUPO low9.62.7
Sequest: Xcorr FDR12.25.2