The EU subsidises the use of skimmed-milk powder (SMP) in compound feeding stuffs. There are indications of falsified SMP content due to the addition of plant proteins. These proteins are not allowed in SMP and cannot be identified by the official reference method. Since soy and pea proteins are most likely to be added to SMP, manufactured SMP containing 1 and 5% of these plant proteins was used to develop a sensitive protein identification method based on mass spectrometry (MS). The method included a pre-fractionation step to enrich for plant proteins by using a borate buffer. A very fast perfusion liquid chromatography method including sensitive and selective intrinsic fluorescence detection was developed for monitoring and quantifying the efficiency of the pre-fractionation and screening for plant proteins. After tryptic digestion of the enriched fraction from manufactured adulterated SMP, numerous peptides originating from the major seed proteins of soy (glycinin, ß-conglycin) and pea (legumin, vicilin) could be identified by MS/MS analysis on a quadrupole time-of-flight MS instrument.