IQcat: Multiplexed Protein Quantification by Isoelectric QconCAT

Expression of isotopically labeled peptide standards as artificial concatamers (QconCATs) allows for the multiplex quantification of proteins in unlabeled samples by mass spectrometry. We have developed a generalizable QconCAT design strategy, which we term IQcat, wherein concatenated peptides are binned by isoelectric point to facilitate MS-sample enrichment by isoelectric focusing. Our method utilizes a rapid (~2 week), inexpensive and scalable purification of arg/lys labeled IQcat standards in the E. coli auxotroph AT713. With this pipeline we assess the fidelity of IQcat-based absolute quantification for 10 yeast proteins over a broad concentration range in a single information-rich isoelectric fraction. The technique is further employed for a quantitative study of androgen-dependent protein expression in cultured prostate cancer cells.