The presented method tackles the problem encountered when trying to quantify the ratio of e.g. two distinct target peptides, like phosphorylated vs. non-phosphorylated peptides. Therefore the method uses chemically synthesized peptides that contain both target peptides separated by a protease recognition site. The peptides are then cleaved by the respective protease, resulting in a mixture of the two target peptides with a stoichiometry defined solely by the design of the original peptide (see figure).
The ratio of the target peptides in a sample can then easily be estimated by double ratio calculation.
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