Quantification of amyloid precursor protein isoforms using quantification concatamer internal standard.

It is likely that expression and/or post-translational generation of various protein isoforms can be indicative of initial pathological changes or pathology development. However, selective quantification of individual protein isoforms remains a challenge, because they simultaneously possess common and unique amino acid sequences. Quantification concatamer (QconCAT) internal standards were originally designed for a large-scale proteome quantification and are artificial proteins that are concatamers of tryptic peptides for several proteins. We developed a QconCAT for quantification of various isoforms of amyloid precursor protein (APP). APP-QconCAT includes tryptic peptides that are common for all isoforms of APP concatenated with those tryptic peptides that are unique for specific APP isoforms. Isotope-labeled APP-QconCAT was expressed, purified, characterized, and further used for quantification of total APP, APP695, and amyloid-β (Aβ) in the human frontal cortex from control and severe Alzheimer's disease donors. Potential biological implications of our quantitative measurements are discussed. It is also expected that using APP-QconCAT(s) will advance our understanding of biological mechanism by which various APP isoforms involved in the pathogenesis of Alzheimer's disease.