Ivory is a highly prized material in many cultures since it can be carved into intricate designs and have a highly polished surface. Due to its popularity, the animals from which ivory can be sourced are under threat of extinction. Identification of ivory species is not only important for CITES compliance, it can also provide information about the context in which a work was created. Here, we have developed a minimally invasive workflow to remove minimal amounts of material from precious objects and, using high-resolution mass spectrometry-based proteomics, identified the taxonomy of ivory and bone objects from The Metropolitan Museum of Art collection dating from as early as 4000 B.C. We built a proteomic database of underrepresented species based on exemplars from the American Museum of Natural History, and proposed alternative data analysis workflows for samples containing inconsistently preserved organic material. This application demonstrates extensive ivory species identification using proteomics to unlock sequence uncertainties, e.g., Leu/Ile discrimination.