PXD050393

PXD050393 is an original dataset announced via ProteomeXchange.

Title	Evaluation of decontamination methods for palaeoproteomic analysis of Pleistocene skeletal proteomes
Description	Palaeoproteomic analysis of skeletal elements is increasingly used to study topics such as human evolution. However, many of the skeletal elements that are analysed have been stored and handled over long time periods, and have therefore accumulated contaminating proteins, which may complicate analysis of the endogenous ancient proteome. In this study, we evaluate five commonly used approaches for decontamination in palaeoproteomics, using a Pleistocene Equus sp. bone that was artificially contaminated with modern dog saliva and fur. First, we show that contamination affects reconstruction of the ancient proteome, even when the potential for contamination is not taken into account. Thereafter, our results show that although most decontamination methods reduce contamination, only a brief bleach wash seemingly returns the proteome to its original composition. None of the decontamination approaches are found to damage the endogenous proteome. Decontamination may, however, significantly improve recovery of low-abundance proteins.
HostingRepository	PRIDE
AnnounceDate	2025-04-24
AnnouncementXML	Submission_2025-04-24_00:46:44.264.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zandra Fagernäs
SpeciesList	scientific name: Equus caballus (Horse); NCBI TaxID: 9796; scientific name: Canis familiaris (Dog) (Canis lupus familiaris); NCBI TaxID: 9615;
ModificationList	dihydroxylated residue; hydroxylated proline; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-06 01:35:36	ID requested
⏵ 1	2025-04-24 00:46:44	announced

10.1016/J.JAS.2025.106228;

submitter keyword: Decontamination,Palaeoproteomics, Archaeology, Pleistocene, Skeletal proteomes

Frido Welker
contact affiliation	Globe Institute, University of Copenhagen, Denmark
contact email	frido.welker@sund.ku.dk
lab head
Zandra Fagernäs
contact affiliation	Globe Institute, University of Copenhagen
contact email	zandra.fagernas@sund.ku.dk
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/2025/04/PXD050393

PRIDE project URI

• PRIDE
  1. PXD050393
     1. Label: PRIDE project
     2. Name: Evaluation of decontamination methods for palaeoproteomic analysis of Pleistocene skeletal proteomes