title: Classification of ancient mammal individuals using dental pulp MALDI-TOF MS peptide profiling.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  We 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
  Mass 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.
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UMR CNRS 6236 IRD 198, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France.
authors.forename: Thi-Nguyen-Ny
authors.initials: TN
authors.lastname: Tran
authors.forename: Gérard
authors.initials: G
authors.lastname: Aboudharam
authors.forename: Armelle
authors.initials: A
authors.lastname: Gardeisen
authors.forename: Bernard
authors.initials: B
authors.lastname: Davoust
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Bocquet-Appel
authors.forename: Christophe
authors.initials: C
authors.lastname: Flaudrops
authors.forename: Maya
authors.initials: M
authors.lastname: Belghazi
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
authors.forename: Michel
authors.initials: M
authors.lastname: Drancourt
mesh_terms: D000818:Animals; D002048:Burial / Q000266:history; D002415:Cats; D002417:Cattle; D002648:Child; D030562:Databases, Protein; D003782:Dental Pulp / Q000737:chemistry* / Q000378:metabolism / Q000473:pathology*; D004285:Dogs; D049690:History, Ancient; D006801:Humans; D008322:Mammals / Q000033:anatomy & histology / Q000145:classification* / Q000378:metabolism; D055442:Metabolome; D010449:Peptide Mapping / Q000379:methods; D010455:Peptides / Q000032:analysis* / Q000378:metabolism; D010802:Phylogeny; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D034421:Sus scrofa
chemical_list: D010455:Peptides