Ac-IP tag enables multiplexed proteome quantification in data-independent acquisition mode

We propose the isotopically labeled Ac-IP (acetyl-isoleucine-proline) tag for multiplexed quantification of peptides at the MS1 level in the data-independent acquisition (DIA) mode. Differentially labeled peptides have distinct precursor ions carrying the quantitative information but identical MS2 spectra. The isotopically labeled Ac-Ile part leaves as a neutral loss upon collision-induced dissociation (CID) while fragmentation of the peptide backbone generates information for peptide identification.