The objectives of this study were to evaluate the influence of different pure pig breeds and muscle types on the expression of muscle proteins, as well as their interactions, and second, to find biomarkers for breed and muscle types. A total of 126 male pigs, including 43 Landrace, 21 Duroc, 43 Large White, 13 Pietrain, and 6 Belgian Landrace, were slaughtered at the age of 174 +/- 6 d. Samples from the semimembranosus muscle (SM) and LM were collected 24 h postmortem. Proteomic spectra were generated on an anion exchanger (Q10), a cation exchanger (CM10), and on immobilized metal affinity capture (IMAC30) ProteinChip arrays and analyzed using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry ProteinChip techniques. Breed and muscle type did not affect the number of peaks per spectrum but, interestingly, affected the average intensity of the peaks. Of these peaks, a total of 4 proved to be potential protein biomarkers to differentiate LM or SM muscles, and 2 to classify specific breed types. Additionally, several peaks influenced by the interaction between muscle and breed types could correctly classify pig muscles according to their breed. Further studies need to be carried out to validate and identify these potential protein biomarkers for breed and muscle types in finishing pigs.