PXD055222

PXD055222 is an original dataset announced via ProteomeXchange.

Title	Classification of Collagens via peptide ambiguation, in a paleoproteomic LC-MS/MS-based taxonomic pipeline
Description	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.
HostingRepository	PRIDE
AnnounceDate	2025-03-16
AnnouncementXML	Submission_2025-03-16_07:41:44.767.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD055222
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Maarten Dhaenens
SpeciesList	scientific name: Dama dama; NCBI TaxID: 30532; scientific name: Cervus; NCBI TaxID: 9859; scientific name: Megaloceros giganteus (Giant deer) (Alces gigantea); NCBI TaxID: 227166; scientific name: Canis lupus; NCBI TaxID: 9612; scientific name: Tinca tinca; NCBI TaxID: 27717; scientific name: Equus caballus (Horse); NCBI TaxID: 9796; scientific name: Panthera spelaea; NCBI TaxID: 2770979; scientific name: Rangifer tarandus (Reindeer) (Cervus tarandus); NCBI TaxID: 9870; scientific name: Esox lucius; NCBI TaxID: 8010; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Mammuthus primigenius; NCBI TaxID: 37349; scientific name: Capreolus capreolus (Roe deer); NCBI TaxID: 9858; scientific name: Lepus europaeus; NCBI TaxID: 9983; scientific name: Barbus barbus barbus; NCBI TaxID: 249161; scientific name: Percidae; NCBI TaxID: 8165; scientific name: Ursus spelaeus; NCBI TaxID: 39097; scientific name: Crocuta crocuta spelaea; NCBI TaxID: 1036967; scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825; scientific name: Lutra lutra (European river otter); NCBI TaxID: 9657; scientific name: Panthera; NCBI TaxID: 9688; scientific name: Meles sp.; NCBI TaxID: 30545; scientific name: Vulpes sp.; NCBI TaxID: 30540; scientific name: Caprinae; NCBI TaxID: 9963; scientific name: Coelodonta antiquitatis (woolly rhinoceros); NCBI TaxID: 222863; scientific name: Arvicolinae; NCBI TaxID: 39087; scientific name: Felis catus (Cat) (Felis silvestris catus); NCBI TaxID: 9685; scientific name: Silurus glanis; NCBI TaxID: 94993; scientific name: Castor fiber (Eurasian beaver); NCBI TaxID: 10185;
ModificationList	methylthiolated residue; monohydroxylated residue; deamidated residue
Instrument	ZenoTOF 7600

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-27 01:33:21	ID requested
⏵ 1	2025-03-16 07:41:45	announced

10.1021/ACS.JPROTEOME.4C00962;

10.6019/PXD055222;

submitter keyword: mesolithic, paleoproteomics, pleistocene, neolithic,Bone, dentine, multi-species

Maarten Dhaenens
contact affiliation	ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Belgium
contact email	maarten.dhaenens@ugent.be
lab head
Maarten Dhaenens
contact affiliation	Faculity of Pharmaceutical Biotechnology
contact email	maarten.dhaenens@ugent.be
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PXD055222

PRIDE project URI

• PRIDE
  1. PXD055222
     1. Label: PRIDE project
     2. Name: Classification of Collagens via peptide ambiguation, in a paleoproteomic LC-MS/MS-based taxonomic pipeline