Table S8 study. (DOC) References Table S5 Results of blindly classification of modern mammal individuals by MALDI-TOF MS. (DOC) Table S6 Results of classification of ancient mammal individuals by MALDI-TOF MS peptide profiling of the dental pulp. (DOC) Table S7 Observed mass to charge ratio of unique species- specific peaks (USSPs) (1000 – 3000 Da) from 13 mammal species. ‘‘m/z’’ values in bold characters have been reported by Buckley M. et al. [7]. (DOC) List of the ancient dental pulp specimens used in the 1. Baker CS (2008) A truer measure of the market: the molecular ecology of fisheries and wildlife trade. Mol Ecol 17: 3985–3998. 2. Bellis C, Ashton KJ, Freney L, Blair B, Griffiths LR (2003) A molecular genetic approach for forensic animal species identification. Forensic Sci Int 134: 99–108. 3. Teletchea F, Maudet C, Hanni C (2005) Food and forensic molecular identification: update and challenges. Trends Biotechnol 23: 359–366. 4. Malmstrom H, Stora J, Dale´n L, Holmlund G, Gotherstrom A (2005) Extensive human DNA contamination in extracts from ancient dog bones and teeth. Mol Biol Evol 22: 2040–2047. 5. Karger A, Bettin B, Lenk M, Mettenleiter TC (2010) Rapid characterisation of cell cultures by matrix-assisted laser desorption/ionisation mass spectrometric typing. J Virol Methods 164: 116–121. 6. Zhang X, Scalf M, Berggren TW, Westphall MS, Smith LM (2006) Identification of mammalian cell lines using MALDI-TOF and LC-ESI-MS/ MS mass spectrometry. J Am Soc Mass Spectrom 17: 490–499. 7. Buckley M, Collins M, Thomas-Oates J, Wilson JC (2009) Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 23: 3843–3854. 8. Raoult D, Aboudharam G, Crubezy E, Larrouy G, Ludes B, et al. (2000) Molecular identification by "suicide PCR" of Yersinia pestis as the agent of medieval black death. Proc Natl Acad Sci USA 97: 12800–12803. 9. Lane N (2009) Biodiversity: On the origin of bar codes. Nature 462: 272–274. 10. Hollemeyer K, Altmeyer W, Heinzle E (2002) Identification and quantification of feathers, down, and hair of avian and mammalian origin using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Chem 74: 5960–5968. 11. Wilm M, Shevchenko A, Houthaeve T, Breit S, Schweigerer L, et al. (1996) Femtomole sequencing of proteins from polyacrylamide gels by nano- electrospray mass spectrometry. Nature 379: 466–469. 12. Humpula JF, Ostrom PH, Gandhi H, Strahler JR, Walker AK, et al. (2007) Investigation of the protein osteocalcin of Camelops hesternus: Sequence, structure and phylogenetic implications. Geochimica et Cosmochimica Acta 71: 5956–5967. 13. Ouedraogo R, Flaudrops C, Ben AA, Capo C, Raoult D, et al. (2010) Global analysis of circulating immune cells by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. PLoS ONE 5: e13691. 14. Hollemeyer K, Altmeyer W, Heinzle E, Pitra C (2008) Species identification of Oetzi’s clothing with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry based on peptide pattern similarities of hair digests. Rapid Commun Mass Spectrom 22: 2751–2767. 15. Blow MJ, Zhang T, Woyke T, Speller CF, Krivoshapkin A, et al. (2008) Identification of ancient remains through genomic sequencing. Genome Res 18: 1347–1353. 16. Gilbert MT, Drautz DI, Lesk AM, Ho SY, Qi J, et al. (2008) Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochon- drial genomes. Proc Natl Acad Sci USA 105: 8327–8332. Mammal Classification by Mass-Spectrometry Acknowledgments The authors acknowledge Dominique Castex, Laboratoire d’Anthropolo- gie, UMR 5199, Bordeaux 1; Benoit Clavel, C.R.A.V.O, Bordeaux, France; and Michel Signoli, Laboratoire d’Anthropologie, UMR 6578 CNRS-EFS-Universite´ de la Me´diterrane´e, Marseille, France, who provided ancient specimens. The authors also thank Philippe Decloque- ment and Sa¨ıd Azza (URMITE, Marseille, France) for their assistance with mass spectrometry and protein extraction. Author Contributions Conceived and designed the experiments: DR MD. Performed the experiments: TNNT CF MB. Analyzed the data: TNNT GA BD JPBA DR MD. Contributed reagents/materials/analysis tools: BD AG JPBA DR MD. Wrote the paper: TNNT MB DR MD. 17. Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC (1984) DNA sequences from the quagga, an extinct member of the horse family. Nature 312: 282–284. 18. Krause J, Orlando L, Serre D, Viola B, Prufer K, et al. (2007) Neanderthals in central Asia and Siberia. Nature 449: 902–904. 19. Kempson IM, Skinner WM, Kirkbride PK, Nelson AJ, Martin RR (2003) Time- of-flight secondary ion mass spectrometry analysis of hair from archaeological remains. Eur J Mass Spectrom (Chichester, Eng) 9: 589–597. 20. Drancourt M, Raoult D (2005) Palaeomicrobiology: current issues and perspectives. Nat Rev Microbiol 3: 23–35. 21. Myers SL, Williams JM, Hodges JS (1999) Effects of extreme heat on teeth with implications for histologic processing. J Forensic Sci 44: 805–809. 22. Anikovich MV, Sinitsyn AA, Hoffecker JF, Holliday VT, Popov VV, et al. (2007) Early upper paleolithic in Eastern Europe and implications for the dispersal of modern humans. Science 315: 223–226. 23. Okiji T (2002) Pulp as a connective tissue. In: Hargreaves KM, Goodis HE, eds. Seltzer and Bender’s Dental Pulp Quintessence Publishing Co, Inc. pp 95–122. 24. Asara JM, Garavelli JS, Slatter DA, Schweitzer MH, Freimark LM, et al. (2007) Interpreting sequences from mastodon and T. rex. Science 317: 1324–1325. 25. Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC (2007) Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 316: 280–285. 26. Buckley M, Kansa SW, Howard S, Campbell S, Thomas-Oates J, et al. (2010) Distinguishing between archaeological sheep and goat bones using a single collagen peptide. J Archaeol Sci 37: 13–20. 27. Organ CL, Schweitzer MH, Zheng W, Freimark LM, Cantley LC, et al. (2008) Molecular phylogenetics of mastodon and Tyrannosaurus rex. Science 320: 499. 28. Haldi J, Wynn W (1963) Protein fractions of the blood plasma and dental pulp fluid of the dog. J Dent Res 42: 1217–1221. 29. Honjo H, Tsubakimoto K, Utsumi N, Tsutsui M (1970) Localization of plasma proteins in the human dental pulp. J Dent Res 49: 888. 30. Kocher TD, Thomas WK, Meyer A, Edwards SV, Paabo S, et al. (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci USA 86: 6196–6200. 31. Sauer S, Freiwald A, Maier T, Kube M, Reinhardt R, et al. (2008) Classification and identification of bacteria by mass spectrometry and computational analysis. PLoS ONE 3: e2843. 32. Catusse J, Strub JM, Job C, Van DA, Job D (2008) Proteome-wide characterization of sugarbeet seed vigor and its tissue specific expression. Proc Natl Acad Sci USA 105: 10262–10267. 33. Garcia JM, Martins MD, Jaeger RG, Marques MM (2003) Immunolocalization of bone extracellular matrix proteins (type I collagen, osteonectin and bone sialoprotein) in human dental pulp and cultured pulp cells. Int Endod J 36: 404–410. 34. Harlamb SC, Messer HH (1996) The identification of proteoglycan associated mRNAS in human dental pulp cells. Archs oral Biol 41: 1097–1100. PLoS ONE | www.plosone.org 7 February 2011 | Volume 6 | Issue 2 | e17319