. Author manuscript; available in PMC: 2014 Mar 1.

Published in final edited form as: J Proteome Res. 2013 Feb 12;12(3):1108–1119. doi: 10.1021/pr300631t

Table 5. Summary of Overlapping Validated PSMs.

Dataset	# of Shared PSMs between PeptideProphet and De-Noise			# of Shared PSMs between Percolator and De-Noise			# of Shared PSMs between PeptideProphet and Percolator
Dataset	Full	Half	Non	Full	Half	Non	Full	Half	Non
Gcn4 LCQ	1314	47	0	1206	42	0	1237	46	1
UPS1 LTQ	399	125	9	276	112	7	270	115	12
Tal08 OriXL MiPS	14528	1041	7	12881	482	0	12767	485	0
PBMC OriXL MiPS	25962	6046	113	23565	4423	88	23431	4566	126
PBMC OriXL MiPS-off	27604	6802	161	24420	5070	143	24247	5204	270
PBMC OriVel MiPS	107595	11149	46	94718	7771	36	93830	8171	112
PBMC OriVelMiPS-off	130259	34738	511	115919	25735	182	114134	29234	1628

Note: Data used in this table are outputs under FDR=0.05