Table 1.

Description of validation sets

Validation seta	Experiment type (ESI)	Proteinsb	Theoretical peptidesc	PS ≥1d	PS ≥2e	Tsf	Mixture complexityg	Database search	Quantification
ISB-18	LC-MS	6	153	100%	100%	17h	Low	Spectrum Mill	XIC
Yeast test	LC-MS	8	226	100%	88%	21h	Medium	Spectrum Mill	XIC
Plasma	LC-MS	14	633	71%	36%	16i	Very High	Spectrum Mill	XIC
Sigma48	LC-MS	16	438	88%	69%	34h	Low	Spectrum Mill	XIC
Plasma Hu14	LC-MS	30	1,403	87%	43%	43h	Very high	Spectrum Mill	XIC
Yeast_2	LC-MS	94	1,930	97%	82%	242h	Medium	Spectrum Mill	XIC
HeLa_1	LC-MS	149	4,944	90%	65%	301h	High	Mascot	MSQuant
HeLa_2	GeLC-MS	300	15,172	86%	54%	498h	High	Mascot	MSQuant
Pull-down	GeLC-MS	172	8,062	92%	68%	358h	Medium	Mascot	MSQuant
Plasma Hu14 SCX	SCX-LC-MS	45	1,935	93%	49%	74h	High	Spectrum Mill	XIC

^aAll validation sets were analyzed using an LTQ-Orbitrap except the plasma and ISB-18 data, which were analyzed using an LTQ-FT.

^bOnly proteins with six or more theoretical peptides (in silico digest) and at least five sequence-identified peptides were considered for validation.

^cIn silico tryptic digest with no missed cleavages and a mass range of 600–2,800 Da.

^dProtein sensitivity (PS). The percent of proteins with one or more peptides predicted by the ESP predictor to be among the five highest responding. The weighted mean of all validation sets based on number of proteins is 89%.

^eThe percent of proteins with two or more peptides predicted by the ESP predictor to be among the five highest responding. The weighted mean of all validation sets based on number of proteins is 60%.

^fTest statistic (Ts). The sum of correctly predicted peptides among the five highest-responding peptides for all proteins in the validation set.

^gSimple comparison of the number of proteins present in each sample mixture. For example, plasma has more than 10,000 proteins (very high) compared to sigma48, which has 48 proteins (low).

^hP < 0.0001

ⁱP = 0.0363 based on null distribution for the entire validation set, by permutation test.