Localization of Organelle Proteins Using Data-Independent Acquisition (DIA-LOP).

ABSTRACT: Subcellular localization within the proteome fundamentally influences cellular processes; however, the development of high-throughput techniques to allow proteome-wide mapping of the cell has proven difficult. Here we present DIA-LOP, an approach capable of high-throughput spatial proteome mapping with in-depth subcellular resolution. This unified framework integrates differential-ultracentrifugation (DC) with ion-mobility-based data-independent acquisition mass spectrometry, alongside data processing using DIA-NN and spatial analysis within the pRoloc bioinformatics pipeline. We obtain the largest DIA-based subcellular proteomics map, with 8242 protein identifications across 13 organellar compartments in U-2 OS cells. Within the same experimental pipeline, we compare DC fractionation with

SUBMITTER: McCaskie K 

PROVIDER: S-EPMC12455123 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature