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Table 2 Number of PSMs output by PeptideProphet, Percolator, and OLCS-Ranker

From: A cost-sensitive online learning method for peptide identification

DatasetMethodFDR = 0.02FDR = 0.04
  TargetsDecoysRatioTargetsDecoysRatio
YeastPepProphet1379130.2061436290.214
 Percolator1225120.1831366270.204
 OLCS-Ranker1374130.2051467290.219
Ups1PepProphet50650.056545110.061
 Percolator47140.052554110.062
 OLCS-Ranker47340.053528100.059
Tal08PepProphet91190.092948200.096
 Percolator1036100.1051059210.107
 OLCS-Ranker1140100.1151156220.117
Tal08-largePepProphet149661520.354155163170.367
 Percolator157931590.374161643290.383
 OLCS-Ranker157061570.372160783270.381
Velos-mipsPepProphet11653311770.55812008024500.575
 Percolator11604611720.55612095224680.579
 OLCS-Ranker11708411820.56112003324480.575
Velos-nomipsPepProphet16679016840.54217393535490.566
 Percolator16517416680.53717436135580.567
 OLCS-Ranker17072217230.55517700736110.576
  1. “Targets”: number of selected target PSMs; “Decoys”: number of selected decoy PSMs; “ratio”: the ratio of the number of selected target PSMs under FDR = 0.04 to the total number of target PSMs in the dataset; “PepProphet”: PeptideProphet