Sika deer (Cervus nippon Temminck) and red deer (Cervus elaphus Linnaeus) are the two creatural sources of velvet antlers, which are recorded in the Chinese Pharmacopoeia (2020 edition). However, the counterfeits-moose (Alces alces Linnaeus) antlers are selling as genuine products in the market. In order to strengthen antler quality control and market supervision, a UHPLC-QTOF-MS coupled with chemometrics analysis and UHPLC-TQS-MS were developed and applied to distinguish the Velvet Antler of moose from that of sika deer and red deer. Firstly, the QTOF-MS quantized data obtained from samples treated with trypsin were subjected to principal component analysis (PCA) to classify these three kinds of antlers. Then, the potential differential marker peptides were found with orthogonal partial least-squares discriminant analysis (OPLS-DA). Finally, validation of these differential marker peptides was assessed using UHPLC-QTOF-MS, and the results showed that the specific ion pairs (m/z 724.8 → 518.1, m/z 724.8 → 938.3, m/z 732.8 → 526.3, m/z 732.8 → 784.3) were detected in moose deer antler, not in velvet antler of sika deer (Cervus nippon Temminck) and red deer (Cervus elaphus Linnaeus). The methods in the paper and specific ion pairs could be successfully applied to distinguish moose antlers from sika deer antlers and red deer antlers.
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