This study tries to fill the knowledge gap regarding differences in the expression of proteins in the meat of European wild boar (Sus scrofa scrofa) and domestic pig (Sus scrofa domestica), considering the impact of thermally induced degradation. We assessed relative protein changes between cooked longissimus thoracis et lumborum (LTL) muscle proteomes by using mass spectrometry, chemometric, label-free proteomic, and bioinformatic tools. Among 30 differentially abundant proteins identified MyHC-2a, ATPs-α, CK-S, ADP/ATPt1, IDH2, and MyBP-C1 were upregulated (x > 1) whereas NEB, γ-ENO and EPSF were downregulated (x < 1) in wild boar. ShinyGO and KEGG database pathway analyses revealed that these proteins are mainly involved in processes related to muscle contraction and various pathways of glucose metabolism and energy production. Protein expression changes could have been caused by the different muscle activity of wild animals in response to prolonged movement associated with foraging for food in the natural environment. Keywords Wild boar Pig Skeletal muscle Heat processing Label-free proteomics LC-Q-TOF