Table 4. Comparison of quantification of abundant plasma proteins by HI3 peptide quantitation and clinical immunoassays.

Protein	HI3 peptide quantitation				Immunoassay			r
	median (ng/mL)	intra-assay CV1(%)	inter-assay CV2(%)	n1	median (ng/mL)	inter-assay CV3(%)	n2
Albumin	7.4 x107	15	12	31	4.7 x107	2	31	0.72
Immunoglobulin γ	4.8 x106	17	30	31	9.6 x106	2	31	0.86
Transferrin	2.7 x106	19	19	31	2.7 x106	2	31	0.75
Fibrinogen	2.6 x106	15	14	30	1.6 x106	3	30	0.81*
Complement C3	2.3 x106	16	17	31	1.0 x106	2	31	0.86
Apolipoprotein A-I	1.7 x106	14	29	31	1.5 x106	4	31	0.86
Haptoglobin	1.3 x106	20	26	31	1.2 x106	2	31	0.92
Apolipoprotein B-100	1.0 x106	15	14	31	0.9 x106	3	31	0.85
Immunoglobulin α	0.7 x106	17	18	31	1.8 x106	1	31	0.93
Complement C4	0.7 x106	16	16	29	0.2 x106	3	31	0.76
Ceruloplasmin	0.4 x106	16	22	31	0.3 x106	5	31	0.89
Immunoglobulin μ	0.2 x106	14	26	31	1.0 x106	3	31	0.96

Median (ng/mL): median of protein concentrations determined from number of samples shown in column n ¹ or n ².Intra-assay CV ¹: coefficient of variation by analysis of 6 aliquots of a pooled plasma sample, digested and injected during 1 day of measurements; Inter-assay CV ² by analysis of 7 aliquots of a pooled sample, digested and injected during a period of 3 months of normal operation. n ¹, the number of samples with proteins quantified by LCMS^E (out of 31). Immunoassay data were obtained from the external quality control assessment scheme of the Stichting Kwaliteitscontrole Medische Laboratoria (SKML) in the Netherlands, data from September 2010. Median concentration of each analyte, inter-institute variation (inter-assay CV ³) and number of samples in which a protein was detected (n ²), are provided. r = Spearman correlation coefficient between label free MS^e and immunoassay values obtained for individual samples, * two outliers were removed, with outliers r = 0.54.