Label free IMS-MSE protein quantification for plant Golgi protein localisation and abundance

Golgi resident proteins in Arabidopsis thaliana are challenging to quantify since the abundance of this organelle is relatively low within the cell. In this study an organelle fractionation approach, targeting the Golgi apparatus, was combined with a label free quantitative MS, data-independent acquisition (DIA) method employing ion mobility separation known as LC-IMS-MSE, to simultaneously localise proteins to the Golgi apparatus and assess their relative quantity. In total 33 proteins were localised to Golgi apparatus and 102 Golgi localised proteins were quantified.