This current study aims to understand the effects of radio frequency (RF) processing, specifically on the protein isolate fraction prepared from pre-treated yellow pea seeds. To characterize these potential changes, a global comparative proteomics study was performed using Tandem Mass Tag (TMT) labeling followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Further, the impacts of the changes in protein composition and structure on the techno-functional and nutritional properties of the isolates were also studied.