Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments.

ABSTRACT: Tandem mass tags (TMTs) 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 in version 3 of the instrument acquisition software Tune. However, 47% of Orbitrap Fusion, Lumos, or Eclipse submissions to PRIDE were generated using prior software versions. To quantify the impact of the notch on existing quantitative proteomics data, we generated a mixed species benchmark and acquired quantitative data using Tune versions 2 and 3. Intensities below the notch are predominantly underestimated with Tune version 2, leading to overesti

SUBMITTER: Smith TS 

PROVIDER: S-EPMC9204819 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature