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Classification of ancient mammal individuals using dental pulp MALDI-TOF MS peptide profiling.

Tran TN, Aboudharam G, Gardeisen A, Davoust B, Bocquet-Appel JP, Flaudrops C, Belghazi M, Raoult D, Drancourt M - PLoS ONE (2011)

Bottom Line: Our work was organized into three successive steps.The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard.The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals.

View Article: PubMed Central - PubMed

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.

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.

Methodology/principal findings: 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/significance: 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.

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MALDI-TOF MS peptide profiling of proteins extracted from dental pulp.Pseudo-gel displays (Gel View, Bruker Daltonics) of the peptide spectra obtained with wild boar (a) and pig (b) specimens were used as the reference peptide. The mass-to-charge ratio (m/z) of each peptide is indicated on the x-axis, and the relative intensity of each peak is shown on the y-axis. Blue bars correspond to peaks from pig specimens, red bars correspond to peaks from wild boar specimens, and green bars represent peaks shared by both.
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pone-0017319-g003: MALDI-TOF MS peptide profiling of proteins extracted from dental pulp.Pseudo-gel displays (Gel View, Bruker Daltonics) of the peptide spectra obtained with wild boar (a) and pig (b) specimens were used as the reference peptide. The mass-to-charge ratio (m/z) of each peptide is indicated on the x-axis, and the relative intensity of each peak is shown on the y-axis. Blue bars correspond to peaks from pig specimens, red bars correspond to peaks from wild boar specimens, and green bars represent peaks shared by both.

Mentions: All MALDI-TOF MS results were in agreement with the observed morphological characteristics and were confirmed by cytochrome b sequencing (Figure 1, Table S1, Table S5, Table S6, Table S8). We therefore successfully classified the remains of individuals representing four domestic mammalian species frequently encountered in excavations. In addition, MALDI-TOF MS analysis of keratin recovered from the clothing of a 5,300-year-old Tyrolean mummy, which was remarkably preserved due to natural freezing in the Alps, revealed that the material originated from sheep and cattle [14]. The results presented here establish the proof-of-concept that MALDI-TOF MS peptide profiling of dental pulp can accurately classify ancient mammals at the species level. The finding that wild boars and pigs, which are members of the same genetic species, had 5 and 2 USSPs from a total of 11 and 12 SEMPs, respectively, illustrates the discriminatory power of MALDI-TOF MS peptide profiling (Figure 3). Ancient mammals were previously identified by analyzing dried muscle and skin from well-preserved museum specimens, hair shafts from permafrost-preserved animals, and bones and teeth of buried animals [15]–[18]. These tissues are directly exposed to the environment; contamination and degradation of surface proteins have been observed [19]. Reduced numbers of USSPs have been identified in tinted or bleached hair samples, and new peaks in these specimens have also been observed [10].


Classification of ancient mammal individuals using dental pulp MALDI-TOF MS peptide profiling.

Tran TN, Aboudharam G, Gardeisen A, Davoust B, Bocquet-Appel JP, Flaudrops C, Belghazi M, Raoult D, Drancourt M - PLoS ONE (2011)

MALDI-TOF MS peptide profiling of proteins extracted from dental pulp.Pseudo-gel displays (Gel View, Bruker Daltonics) of the peptide spectra obtained with wild boar (a) and pig (b) specimens were used as the reference peptide. The mass-to-charge ratio (m/z) of each peptide is indicated on the x-axis, and the relative intensity of each peak is shown on the y-axis. Blue bars correspond to peaks from pig specimens, red bars correspond to peaks from wild boar specimens, and green bars represent peaks shared by both.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3045434&req=5

pone-0017319-g003: MALDI-TOF MS peptide profiling of proteins extracted from dental pulp.Pseudo-gel displays (Gel View, Bruker Daltonics) of the peptide spectra obtained with wild boar (a) and pig (b) specimens were used as the reference peptide. The mass-to-charge ratio (m/z) of each peptide is indicated on the x-axis, and the relative intensity of each peak is shown on the y-axis. Blue bars correspond to peaks from pig specimens, red bars correspond to peaks from wild boar specimens, and green bars represent peaks shared by both.
Mentions: All MALDI-TOF MS results were in agreement with the observed morphological characteristics and were confirmed by cytochrome b sequencing (Figure 1, Table S1, Table S5, Table S6, Table S8). We therefore successfully classified the remains of individuals representing four domestic mammalian species frequently encountered in excavations. In addition, MALDI-TOF MS analysis of keratin recovered from the clothing of a 5,300-year-old Tyrolean mummy, which was remarkably preserved due to natural freezing in the Alps, revealed that the material originated from sheep and cattle [14]. The results presented here establish the proof-of-concept that MALDI-TOF MS peptide profiling of dental pulp can accurately classify ancient mammals at the species level. The finding that wild boars and pigs, which are members of the same genetic species, had 5 and 2 USSPs from a total of 11 and 12 SEMPs, respectively, illustrates the discriminatory power of MALDI-TOF MS peptide profiling (Figure 3). Ancient mammals were previously identified by analyzing dried muscle and skin from well-preserved museum specimens, hair shafts from permafrost-preserved animals, and bones and teeth of buried animals [15]–[18]. These tissues are directly exposed to the environment; contamination and degradation of surface proteins have been observed [19]. Reduced numbers of USSPs have been identified in tinted or bleached hair samples, and new peaks in these specimens have also been observed [10].

Bottom Line: Our work was organized into three successive steps.The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard.The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals.

View Article: PubMed Central - PubMed

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.

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.

Methodology/principal findings: 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/significance: 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.

Show MeSH
Related in: MedlinePlus