IQ cat: Multiplexed protein quantification by isoelectric Q con CAT

Expression of isotopically labeled peptide standards as artificial concatamers ( Q con CAT s) allows for the multiplex quantification of proteins in unlabeled samples by mass spectrometry. We have developed a generalizable Q con CAT design strategy, which we term IQ cat, wherein concatenated peptides are binned by p I to facilitate MS ‐sample enrichment by isoelectric focusing. Our method utilizes a rapid (∼2 weeks), inexpensive and scalable purification of arg/lys labeled IQ cat standards in the Escherichia coli auxotroph AT 713. With this pipeline, we assess the fidelity of IQ cat‐based absolute quantification for ten 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.