[en] Liquid chromatography-mass spectrometry (LC-MS/MS) extends the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) Zooarcheology by Mass Spectrometry (ZooMS) "mass fingerprinting" approach to species identification by providing fragmentation spectra for each peptide. However, ancient bone samples generate sparse data containing only a few collagen proteins, rendering target-decoy strategies unusable and increasing uncertainty in peptide annotation. To ameliorate this issue, we present a ZooMS/MS data pipeline that builds on a manually curated Collagen database and comprises two novel algorithms: isoBLAST and ClassiCOL. isoBLAST first extends peptide ambiguity by generating all "potential peptide candidates" isobaric to the annotated precursor. The exhaustive set of candidates created is then used to retain or reject different potential paths at each taxonomic branching point from superkingdom to species, until the greatest possible specificity is reached. Uniquely, ClassiCOL allows for the identification of taxonomic mixtures, including contaminated samples, as well as suggesting taxonomies not represented in sequence databases, including extinct taxa. All considered ambiguity is then graphically represented with clear prioritization of the potential taxa in the sample. Using public as well as in-house data acquired on different instruments, we demonstrate the performance of this universal postprocessing and explore the identification of both genetic and sample mixtures. Diet reconstruction from 40,000-year-old cave hyena coprolites illustrates the exciting potential of this approach.
Disciplines :
Archaeology Laboratory medicine & medical technology
Author, co-author :
Engels, Ian ; ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent 9000,Belgium
Burnett, Alexandra ; ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent 9000,Belgium ; ArcheOs Laboratory for Biological Anthropology, Faculty of Arts and Philosophy, Ghent University, Ghent 9000, Belgium
Robert, Prudence; ArcheOs Laboratory for Biological Anthropology, Faculty of Arts and Philosophy, Ghent University, Ghent 9000, Belgium
Pironneau, Camille; ArcheOs Laboratory for Biological Anthropology, Faculty of Arts and Philosophy, Ghent University, Ghent 9000, Belgium
Abrams, Grégory; ArcheOs Laboratory for Biological Anthropology, Faculty of Arts and Philosophy, Ghent University, Ghent 9000, Belgium ; Scladina Cave Archaeological Centre, Espace muséal d'Andenne, Andenne 5300, Belgium
Bouwmeester, Robbin ; VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium ; Department of Biomolecular Medicine, Ghent University, Ghent 9052 Belgium
Van der Plaetsen, Peter
Di Modica, Kévin; Scladina Cave Archaeological Centre, Espace muséal d'Andenne, Andenne 5300, Belgium
Otte, Marcel
Straus, Lawrence Guy; Dept. of Anthropology, MSC01 1040, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
Fischer, Valentin ; Université de Liège - ULiège > Département de géologie > Evolution and diversity dynamics lab
Bray, Fabrice ; CNRS, UAR 3290 - MSAP - Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Univ. Lille, Lille F-59000, France
Mesuere, Bart ; VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium ; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent B-9000, Belgium ; Department of Biochemistry, Ghent University, Ghent B-9000 Belgium
De Groote, Isabelle; ArcheOs Laboratory for Biological Anthropology, Faculty of Arts and Philosophy, Ghent University, Ghent 9000, Belgium ; School of Biological and Environmental Sciences, Research Centre in Evolutionary Anthropology and Palaeoecologys, Liverpool John Moores University, Liverpool L3 3AF, U.K
Deforce, Dieter; ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent 9000,Belgium
Daled, Simon ; ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent 9000,Belgium
Dhaenens, Maarten ; ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent 9000,Belgium
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