The present study used a proteomic data set obtained from a 2 x 2 x 2 factorial experiment on longissimus muscle of 24 pigs to identify single or couples of proteins allowing correct classification of pigs according to gender, sire breed, or rearing environment. An actin isoform, a myosin light chain 2 isoform and cytochrome Bc1 allowed each, correct classification of all pigs according to gender. Peroxiredoxin 6 allowed correct classification of 23 pigs according to indoor or outdoor rearing environment, but only if gender was also taken into account. Heat shock protein 73 allowed correct classification of 21 pigs according to sire breed, Duroc or Large White. Results show that proteins may be used as biomarkers for traceability or genetic research. Relationships between treatment factors and intracellular regulatory mechanisms associated with these proteins are discussed.