High-grade serous ovarian cancer (HGSC) has a disproportionate impact on cancer-related mortality in women. There is an urgent need to improve treatment options for HGSC. This includes better selection of patients who will benefit from existing treatments, including HRD targeted therapy, and discovery of new targeted therapeutic options. Reliable tissue-based biomarkers that can guide treatment selection are key to progress in this area. A challenge for their definition is the large volume of disease that is characteristically present at HGSC diagnosis and that can show considerable heterogeneity within and between anatomical sites. In order to address this issue, we carried out a detailed study of the HGSC proteome in eleven individuals by comparing genomic and gene-expression features with multiple independent proteomic results derived from fresh frozen (FF) and formalin fixed paraffin embedded (FFPE) samples from both ovary and a common metastatic site, omentum. Our findings gave emphasis to the influence of sample site of origin on biomarker expression, and revealed opportunities to detect mechanisms shaping the HGSC tumour immune microenvironment from tissue proteomics. The dataset also forms a useful resource to investigate molecular heterogeneity in HGSC.