Pulses are normally processed prior to consumption, are high in protein, providing opportunities for improving nutritional qualities of food. Processing methods can modify nutritional properties, affecting protein content, composition and functionality. In this study, we investigated the effect of processing methods on protein concentration and yield from protein isolates prepared by alkaline solubilisation and isoelectric precipitation, from whole seed flour, raw dahl flour, roasted dahl flour and germinated flour of mungbean. Protein isolates contained protein contents ranging from 87.3 to 90.4 g 100 g-1. The effect of processing methods on protein solubility characteristics was evident, as protein yields ranged from 75.7 (whole seed flour), 80.8 (raw dahl flour), 27.1 (roasted dahl flour) and 65.9 g 100 g-1 (germinated seed flour). Essential amino acid content was higher in protein isolates prepared from germinated flour, at 30.03 g 100 g-1 (39.1% of amino acids), compared to raw dahl flour, at 27.08 g 100 g-1 (38.3% of amino acids). A comparative proteomic analysis of protein isolates, prepared from raw dahl and germinated flour, resulted in the inferred identification of 214 proteins from protein sequence databases, in which, 72 proteins were classified as being common, 42 proteins specific to raw dahl flour and 28 proteins specific to germinated flour. Processing methods such as roasting and germination can significantly alter flour protein solubility, consequently, impacting on overall efficiency of protein extraction. The comparative proteomic analysis used in this study proved to be useful for investigating changes in protein composition and relative abundance, highlighting the potential in applying this technology for further characterisation of modified protein fractions for food applications.