. Author manuscript; available in PMC: 2011 Oct 1.

Published in final edited form as: J Proteome Res. 2010 Oct 1;9(10):5133–5141. doi: 10.1021/pr100409r

Table 1. Evaluation of different thresolds based on spectral-count-derived p values¹.

Threshold	# proteins passing the threshold

	Null experiments			Control-ALS comparisons

	C1 vs C2	A1 vs A2	#False²	C1 vs A1	C2 vs A2	#Accepted³	FDR⁴
0.2	329	340	18	319	514	92	19.6%
0.15	287	291	10	273	470	74	13.5%
0.1	168	190	3	160	332	45	6.7%
0.09	167	188	2	159	331	45	4.4%
0.08	149	170	2	147	313	44	4.5%
0.07	146	163	2	141	304	40	5.0%
0.06	143	156	2	136	294	38	5.3%
0.05	135	153	0	133	292	38	0.0%
0.04	102	105	0	93	213	29	0.0%
0.03	95	100	0	86	201	24	0.0%
0.02	86	82	0	77	185	22	0.0%
0.01	60	56	0	54	140	20	0.0%
0.005	51	42	0	42	107	15	0.0%
0.001	35	29	0	31	72	12	0.0%

The analysis is based on pair-wise comparisons (control: C1 & C2; ALS mice: A1 & A2).

False positives are changed in both null comparisons (C1 vs C2; A1 vs A2).

Proteins are consistently altered in both comparisons (C1 vs A1; C2 vs A2).

⁴

FDR (false discovery rate) = #False/#Accepted

Table 1. Evaluation of different thresolds based on spectral-count-derived p values1.