Tandem mass tags (TMT) enable simple and accurate quantitative proteomics for multiplexed samples by relative quantification of tag reporter ions. Orbitrap™ quantification of reporter ions has been associated with a characteristic notch region in intensity distribution, within which few reporter intensities are recorded. This has been resolved with updated instrument acquisition software, however, 53 % of Orbitrap submissions to PRIDE were generated using the prior software versions. To quantify the impact of the notch on existing quantitative proteomics data, we generate a mixed species benchmark and acquired quantitative data using the outdated software version. Sub-notch intensities are systemically underestimated, leading to over-estimation of the true differences in intensities between samples. However, when summarising reporter ion intensities to higher level features, such as peptides and proteins, few features are significantly affected. The analysis of benchmark dataset indicates that the targeted removal of spectra with reporter ion intensities below the notch is not beneficial for differential peptide or protein testing. Overall, we find the systematic quantification bias associated with the notch is not detrimental for typical proteomics experiments