Table I

Summary of search results and Sequest scoring matrices

AlgorithmScoreMS2 FDRTargetDecoyProtein FDREstimated true proteins
MS2 hitsDistinct peptidesProteinsMS2 hitsDistinct peptidesProteins
%%
MascotIdentity0.6026,5969,1731,8807949485.001,784
MascotIdentity and homology0.2025,8028,9521,8352418181.901,799
Mascot expectation0.1251.0029,4639,9422,00115498979.201,807
OMSSA (expectation)0.031.0048,32813,5122,7252461271278.902,471
X! Tandem (expectation)0.0251.0031,36710,7622,08915712011910.801,851
Sequest p (probability)5 × 10−61.0927,4319,8062,08215111211010.001,862
Sequest HUPO highHUPO high confidence4.8036,84411,8922,90290887263435.901,634
Sequest HUPO lowHUPO low confidence13.5043,19912,3484,5083,1282,7762,09563.50318
Sequest Xcorr FDRXcorr-based FDR1.2024,57510,4602,0071531521059.901,797
ΔCnXcorrRSp
1+2+3+
HUPO high confidence0.11.92.23.754
HUPO low confidence0.11.522.5NAa
Xcorr-based FDR0.12.93.13.7NA
  • a NA, not applicable.