Updated project metadata. Stable isotope labelling of peptides using isobaric reagents such as iTRAQ and TMT enables the multiplexed analysis of proteomes with deep quantitative coverage. Isobaric tagging demonstrates high precision but imperfect accuracy due to ratio underestimation caused by co-fragmentation of ions with mass-to-charge ratios within the isolation window of the targeted precursors. Prompted by empirical observations of isobaric-labelled peptide MS2 spectra, we argue that although a very narrow isolation window will result in severe loss of backbone fragment ions, rendering the spectra unsuitable for peptide identification, the reporter ion signals will remain intense enough to generate quantitative information for a significant portion of the spectra. Based on this assumption we have designed a Dual Isolation Width Acquisition (DIWA) method, in which each precursor is first fragmented with HCD using a standard isolation width for peptide identification and preliminary quantification followed by a concomitant MS2 HCD fragmentation using a much narrower isolation width for the acquisition of quantification-only spectra with reduced interference. We leverage the quantitative values obtained by the “narrow” scans to build linear regression models and apply these to decompress the fold-changes measured at the “standard” scans. Here, we evaluate the DIWA method using a two species TMT-6plex model and discuss the potential of this approach.