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

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 an alternate detergent-based protocol using either DIA or data-dependent acquisition (DDA) mass spectrometry approaches, highlighting the increased subcellular resolution of the DC approach and the increased proteome coverage when DIA is applied. We demonstrate the ability of DIA-LOP to inform clinical studies by identifying and mapping disease-related proteins within our osteosarcoma cell model. With impressive coverage and resolution, DIA-LOP provides a straightforward, high-throughput tool for biochemical discovery. This study thus informs potential users of subcellular proteomics strategies that employ biochemical fractionation of the optimal workflows to achieve high proteome coverage and subcellular resolution.