Localisation of Organelle Proteins using Data-Independent Acquisition (DIA-LOP)

Subcellular localisation 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 with ion-mobility-based data independent acquisition (DIA) mass spectrometry, alongside data processing using DIA-NN and spatial analysis within the pRoloc bioinformatics pipeline. Within the same experimental pipeline, we compare Differential-ultraCentrifugation (DC) fractionation with an alternate detergent-based protocol using both data-dependent (DDA) and data-independent acquisition (DIA) mass spectrometry approaches highlighting the increased subcellular resolution of the DC approach and the increased proteome coverage when DIA is applied. 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.