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Abstract
BackgroundThe classification of ancient animal corpses at the species level remains a challenging task for forensic scientists and anthropologists. Severe damage and mixed, tiny pieces originating from several skeletons may render morphological classification virtually impossible. Standard approaches are based on sequencing mitochondrial and nuclear targets.Methodology/Principal FindingsWe present a method that can accurately classify mammalian species using dental pulp and mass spectrometry peptide profiling. Our work was organized into three successive steps. First, after extracting proteins from the dental pulp collected from 37 modern individuals representing 13 mammalian species, trypsin-digested peptides were used for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard. Second, using a 279–modern spectrum database, we blindly classified 33 of 37 teeth collected in 37 modern individuals (89.1%). Third, we classified 10 of 18 teeth (56%) collected in 15 ancient individuals representing five mammal species including human, from five burial sites dating back 8,500 years. Further comparison with an upgraded database comprising ancient specimen profiles yielded 100% classification in ancient teeth. Peptide sequencing yield 4 and 16 different non-keratin proteins including collagen (alpha-1 type I and alpha-2 type I) in human ancient and modern dental pulp, respectively.Conclusions/SignificanceMass spectrometry peptide profiling of the dental pulp is a new approach that can be added to the arsenal of species classification tools for forensics and anthropology as a complementary method to DNA sequencing. The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals.
Highlights
Classifying the remains of animals at the species level is an important task in various fields of research, such as zooarcheology, anthropology and related applied sciences, including forensic sciences and the surveillance of wildlife trade and endangered species [1,2,3]
Recent work has demonstrated that protein profiles obtained after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of cultured cells can accurately determine the species origin of the cell line [5,6]
Same peaks that were observed in all of ten negative controls were contaminants composed of autoproteolytic trypsin digest fragments (1,726– 2,284 Da) and keratin peaks (1,266–2,824 Da) [10,11] and some additional non-specific peaks (707.3–3,807 Da) with a signal-tonoise ratio (SNR)#3 were probably derived from the column used for the reverse-phase protein purification or from sample preparation
Summary
Classifying the remains of animals at the species level is an important task in various fields of research, such as zooarcheology, anthropology and related applied sciences, including forensic sciences and the surveillance of wildlife trade and endangered species [1,2,3] This could, be a challenging task, as species classification based on morphological characteristics lacks specificity and is of little use with fragmented or severely damaged material, such as a mixture of small skeletal pieces from several individuals [2]. Recent work has demonstrated that protein profiles obtained after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of cultured cells can accurately determine the species origin of the cell line [5,6] This approach is very promising, as MALDI-TOF MS is an easy-to-run and rapid method of analysis. Standard approaches are based on sequencing mitochondrial and nuclear targets
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