Classification of Collagens via peptide ambiguation, in a paleoproteomic LC-MS/MS-based taxonomic pipeline

ABSTRACT: LC-MS/MS extends the MALDI-TOF 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.

INSTRUMENT(S): ZenoTOF 7600

ORGANISM(S): Tinca Tinca Esox Lucius Arvicolinae Castor Fiber (eurasian Beaver) Caprinae Capreolus Capreolus (roe Deer) Crocuta Crocuta Spelaea Sus Scrofa Domesticus (domestic Pig) Lepus Europaeus Meles Sp. Ursus Spelaeus Coelodonta Antiquitatis (woolly Rhinoceros) Panthera Canis Lupus Equus Caballus (horse) Silurus Glanis Percidae Felis Catus (cat) (felis Silvestris Catus) Lutra Lutra (european River Otter) Barbus Barbus Barbus Panthera Spelaea Vulpes Sp. Dama Dama Megaloceros Giganteus (giant Deer) (alces Gigantea) Bos Taurus (bovine) Mammuthus Primigenius Rangifer Tarandus (reindeer) (cervus Tarandus) Cervus

TISSUE(S): Bone, Tooth

SUBMITTER: Maarten Dhaenens  

LAB HEAD: Maarten Dhaenens

PROVIDER: PXD055222 | Pride | 2025-03-14

REPOSITORIES: Pride