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

Table 1

The five unlabeled protein samples from culture S or R, the five protein sample preparation replicates of the labeled proteins from culture C, and the corresponding 20 quantitation categories (see Methods)^a.

	Unlabeled protein sample from culture S or R					[^15N]-labeled protein sample from control culture C
	SP	RP	SA	SB	SC	cSP	cRP	cSA	cSB	cSC
Quantitation category	SP,1	RP,1	SA,1	SB,1	SC,1	cSP,1	cRP,1	cSA,1	cSB,1	cSC,1
	SP,2	RP,2	SA,2	SB,2	SC,2	cSP,2	cRP,2	cSA,2	cSB,2	cSC,2

^aS_A, S_B, and S_C were the unlabeled protein samples from the S culture triplicates. S_P was the pool of S_A, S_B, and S_C. R_P was the pool of the unlabeled proteins from the culture R triplicates. The subscripts “1” and “2” represent the LC/MS duplicates. Only the 3rd gel fraction for samples S_A, S_B, and S_C along with the labeled control in them was analyzed by LC/MS. All of the five gel fractions were analyzed with LC/MS for samples S_P and R_P along with the labeled control in them.