Collagen and gelatine have many applications in the food and pharmaceutical industries. The diversity of their sources raises concerns among consumers and regulatory bodies regarding the authenticity of the products on the market, especially from religious, health and economic perspectives. In this study, commercially processed collagen and gelatine powders were examined using both non-targeted liquid chromatography–high resolution quadrupole time-of-flight tandem mass spectrometry (LC-HR-Q-TOF-MS/MS) and real-time polymerase chain reaction (rt-PCR) for the nuclear myostatin and PLAG1 genes using TaqMan probes. Only six samples yielded a sufficient concentration of good-quality DNA for use in real-time PCR with the universal mammalian myostatin marker. Proteomic analysis enabled the identification of processing-stable markers specific to connective tissue proteins of a given species – for collagen subunits (alpha chains of collagen types I, III, VI, IX and XIV) and non-collagenous proteins (decorin, osteoglycin, prolargin, asporin, fibrillin, matrilin, anchorin, chondroadherin, and calsequestrin). Among collagen subunits suitable for authenticity testing were specific to Sus scrofa COL6A1, COL6A3 COL14A1; Gallus gallus COL6A1, COL6A3 and COL9A1; Pangasianodon hypophthalmus COL1A1B; and Gadus morhua COL1A1A and COL1A2. The results highlight better performance and sensitivity of the proteomic method.