A rapid and highly reproducible gel-eluted liquid fraction entrapment electrophoresis (GELFrEE) coupled with MALDI-TOF mass spectrometry is explored for the first time for authenticating adulteration of pork with water buffalo meat. The GELFrEE offers novel in-solution protein fractionation with a dynamic range from 3.5–500 kDa and the specificity sufficient to be implemented effectively for the identification of species-specific peptides derived from myoglobin (‘HPGDFGADAQGAMSK’, ‘HPSDFGADAQAAMSK’) and carbonic anhydrase-3 (‘GGPLTAAYR’, ‘GGPLAAPYR’) demonstrating their potential as heat-stable markers for meat authentication including commercial samples. The suitability of 2-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF MS for efficiently detecting myosin light chain isoforms from contaminating pork in buffalo meat is also demonstrated. The GELFrEE and gel-based 2-DE approaches efficiently authenticate raw and heat-processed meat and meat mixes up to 0.5% (w/w) level; however, quick extraction protocol and rapid fractionation by GELFrEE offer better solutions for routine MS-based approaches to address global meat fraud issues.