Table 2.

The number of spectra acquired and peptides identified per experiment

Experiment	numSpec(P > 0.0)	numSpec(P > 0.9)	numDistinctPeptides(cumulative, P > 0.9)
gricat	24,833	2,585	734
cdc15_cdc23_newICAT	172,938	22,269	2,889
cdc15_cdc23_oldICAT	156,353	8,281	3,184
cdc15_cdc23_ICAT	21,392	3,337	3,293
cdc23_amf_newICAT	127,673	25,861	4,096
contFFE2Murea	105,686	5,473	4,430
FFEY1	64,880	2,966	5,994
FFEY1Scx	7,045	796	6,396
FFEY2	60,140	7,159	8,877
PeteryeastIcatstdFFE	136,563	4,680	9,375
TSAAT000c	217,919	43,628	11,423
TSAAT030c	249,774	42,519	12,042
TSAAT060c	214,851	28,089	12,424
TSAAT090c	198,057	31,428	13,247
TSAAT120c	179,408	26,182	13,588
TSAAxT000old	101,166	6,311	13,728
T00	94,208	9,206	13,840
T30	83,758	8,758	13,935
T50	106,572	4,606	14,026
opd00034_YEAST	24,049	4,554	14,557
opd00035_YEAST	23,715	3,931	14,862
peroximalPrep0702	24,209	3,197	15,236
Comp12vs12sizefrac	28,926	11,703	17,553
pxproteome	23,720	1,552	17,724
Comp12vs12standSCX	31,652	12,103	18,966
YeastICAT	55,922	6,760	19,577
PvM1	3,796	323	19,623
peroximal_clICAT	92,721	3,693	19,778
Ac30	255,937	37,873	20,025
yeast	140,567	29,411	24,548
gel_msms	343,654	43,022	32,450
mudpit	36,599	10,811	32,859
ipg_ief	136,209	27,792	33,383
rp_int_selected	53,358	14,669	33,684
rp_mass_selected	71,151	4,881	33,857
sdspage	92,802	19,208	34,734
YM_N14N15_DAYGly	38,951	1,658	34,806
YM_N14N15_DAYSer	39,315	1,862	34,843
YM_N14N15_SCYGly	37,124	1,364	34,861
YM_N14N15_SCYSer	37,658	2,238	34,902
APEX_04-22	38,334	1,732	34,926
APEX_04-23	38,175	1,775	34,949
APEX_04-24	36,407	1,359	34,963
APEX_04-28	40,612	2,248	34,995
YeastSCXReps	118,083	60,568	35,446
FFE_nonICAT	21,054	6,870	36,133

Column 1 is the experiment name, column 2 is the number of spectra associated with PeptideProphet probabilities >0, column 3 is the number of spectra associated with PeptideProphet probabilities >0.9, and column 4 is the cumulative number of distinct peptides with PeptideProphet probabilities >0.9.