Assigning Significance in Label-Free Quantitative Proteomics to Include Single-Peptide-Hit Proteins with Low Replicates

Table 4

Numbers of differentially regulated proteins selected with fold-change threshold alone or in combination with MPSP.

Fold change	FP, P, and FDR	Fold-change					Fold-change-MPSP
		Permuted samplepairings				Average
		I	II	III	IV
2	FP (cSP/cRP)	68	77	118	45	77	22
	P (SP/RP)	171	154	186	147	165	104
	FDR	0.40	0.50	0.63	0.31	0.47	0.21
3	FP (cSP/cRP)	30	33	47	20	33	9
	P (SP/RP)	66	70	85	60	70	42
	FDR	0.45	0.47	0.55	0.33	0.47	0.21
4	FP (cSP/cRP)	17	24	32	10	21	1
	P (SP/RP)	42	50	53	35	45	26
	FDR	0.40	0.48	0.60	0.29	0.47	0.04