Fig. 3.

Simulated data based on the developed framework of cost analysis showing the effect of the number of samples and the number of proteins quantified using different absolute quantitative techniques evaluated in four different scenarios. To achieve the same level of precision, two technical replicates are used for isotope-labeled standards-based methods and three technical replicates are used for label-free methods. The first scenario (a) shows AQUA as the ideal method for quantification of one protein in a large number of samples (screening). AQUA and QconCAT present a comparable choice for routine quantification of about 10 proteins in different numbers of samples (b). In the third scenario (c) QconCAT is the cheapest choice for quantification of a defined set of proteins (such as enzymes and transporters) in different numbers of samples. Label-free and QconCAT are the most cost-effective methods for quantification of 500 proteins or more (whole or sub-proteome) in different numbers of samples (d)