A nontargeted protein identification method was developed to screen for adulterations in skimmed-milk powder (SMP). There are indications of falsified SMP content due to the addition of plant proteins. To demonstrate the reliability and accuracy of the developed comparative LC-MS method using a quadrupole TOF MS instrument, adulterated SMP samples were prepared by the addition of protein isolates of soy and pea to skimmed-milk before pasteurisation and evaporation. The comparative LC-MS approach enabled unequivocal discrimination of those SMP samples containing soy and pea protein from nonadulterated SMP. To identify the source of (plant) proteins present in the adulterated SMP, data-dependent LC-MS/MS was used in combination with an include list of differential peptides. Numerous peptides originating from the major seed proteins of soy (glycinin, beta-conglycin) and pea (legumin, vicilin) could be identified in this way.