In recent years, interest and consumption of plant-based proteins have increased significantly. This growth is largely due to environmental, health, and ethical concerns associated with animal-based proteins. Among plant-based options, legumes have gained significant attention as a sustainable and nutrient rich protein source. Despite the growing interest in legumes, seed proteomics has mainly focused on the major seed storage proteins by applying gel-based techniques rather than the global proteome. However, this type of analysis is limited by its dynamic range, which can restrict the detection and accurate quantification of low abundant proteins. Studying the global proteomic profile of legumes is important, as even low abundant proteins may significantly contribute to bioactivity, techno-functional properties and overall amino acid composition. An integrated approach of gel-based and gel-free methods, including high resolution LC-MS/MS, were used throughout this work to profile the global seed proteome of faba bean, lupin and pea as impacted by variety, preprocessing and protein purification methods. Several varieties of Irish grown faba bean (n = 7), lupin (n = 3) and pea (n = 2) were analysed using label-free quantitative proteomic analysis which revealed 245, 117 and 120 proteins differentially abundant across the varieties of each species respectively. These proteins included both major seed storage proteins and other minor seed proteins. This type of analysis allowed for the determination of cultivars with distinct protein profiles such as the faba bean variety Augusta which had significantly lower levels of albumin proteins compared to other varieties. Subsequent trypsin inhibitory activity assays were also applied which revealed a correlation between the levels of albumin protein and trypsin inhibitory activity. The protein purification method (alkaline solubilisation and acid precipitation) used to generate high protein material was shown using LFQ LCMS/ MS to have a larger impact on protein profiles than variety across all three legume species. ASAP purification caused a reduction in the levels of albumin, LEA and trypsin inhibitor proteins as they remained soluble during the acid precipitation step. Species specific impacts of ASAP purification were also revealed using this analysis with lipoxygenase proteins enriched in pea protein isolates relative to their proportion in their respective flours. Using a novel quantification method the ASAP purification method was shown to have an impact on the levels of the faba bean specific antinutritional factor, vicine, with levels reducing by up to 93 %. Pre-processing methods applied prior to purification techniques were shown to have an impact on the protein profile of material. The protein material generated from the dehulled bean was shown to have the most distinct protein profile. This approach also allowed for the characterisation of legume hull material which is largely unexplored and was shown to be enriched in proteolysis related proteins. This analysis allowed for the detection of a large subset of proteins that are uniquely detected in the hull material which could be explored for potential industrial uses. Additionally, the combined proteomic approach used in this work revealed that the faba bean hull material exhibited a large amount of protein aggregation, which was not observed in the hull material of pea and lupin. The work in this thesis expanded the proteomic knowledge of legumes and how they are impacted by variety, purification and pre-processing methods.