Quantitative Proteomics via High Resolution MS Quantification: Capabilities and Limitations

Table 1

Reproducibility estimates from fifteen repeated injections of sixlog mix. Top row are results from an LTQ-Orbi/Velos and bottom row are results from an identical experiment conducted on an LTQ-Orbi/Elite. Peptide selections were done using the model based approach. While 𝛼-casein is reported here we question the absolute amount in the sixlog mix (50 amol) based on the large number of peptides identified and the possibility of copurification from the more abundant components.

Protein	Number selected/; number of total peptides	Median peptide CV (%)	Mean of all peptides CV (%)	Mean of model based selected peptides CV (%)
𝛽-Lactoglobulin (500 fmol)	20/725	42.7	23.4	4.9
	20/1033	19.0	8.2	3.1
Lactoperoxidase (50 fmol)	20/248	21.2	13.9	4.2
	20/482	21.2	9.6	4.0
Carbonic anhydrase (5 fmol)	20/49	15.6	16.1	5.5
	20/84	20.2	12.3	3.4
Glutamate dehydrogenase (500 amol)	11/27	42.1	29.1	11.3
	6/26	50.3	63.5	3.4
𝛼-casein (50 amol)	17/32	26.4	22.7	10.4
	29/42	18.7	13.5	7.3