Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics.

ABSTRACT: Knowledge of intracellular location can provide important insights into the function of proteins and their respective organelles, and there is interest in combining classical subcellular fractionation with quantitative mass spectrometry to create global cellular maps. To evaluate mass spectrometric approaches specifically for this application, we analyzed rat liver differential centrifugation and Nycodenz density gradient subcellular fractions by tandem mass tag (TMT) isobaric labeling with reporter ion measurement at the MS2 and MS3 level and with two different label-free peak integration approaches, MS1 and data independent acquisition (DIA). TMT-MS2 provided the greatest proteome coverage, but ratio compression from contaminating background ions resulted in a narrower accurate dynamic r

SUBMITTER: Tannous A 

PROVIDER: S-EPMC8063867 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature