PXD031386

PXD031386 is an original dataset announced via ProteomeXchange.

Title	Extinct species identification from late Middle Pleistocene and earlier Upper Pleistocene bone fragments and tools not recognizable from their osteomorphological study by an enhanced proteomics protocol
Description	Ancient preserved molecules offer the opportunity of gaining a deeper knowledge on their biological past. However, the development of a proteomic workflow remains a challenge. The analysis of fossils must involve a low quantity of material to avoid damaging the samples. In this study an enhanced proteomic protocol was applied to 5-milligram samples of about 130,000-year-old mammalian bones ranging from the end of the Middle Pleistocene up to the earlier Upper Pleistocene, excavated from Scladina Cave (Sclayn, Belgium). Using sequence homology with modern sequences, a biological classification was successfully achieved and the associated taxonomic ranks to each bone were identified consistently with the information gained from osteomorphological studies and palaeoenvironmental and palaeodietary data. Amino acid substitutions on collagens were identified, thus providing new information on extinct species sequences and helping in taxonomy-based clustering. Considering samples with no osteomorphological information, such as two bone retouchers, proteomics successfully identified the families providing paleontologists new information on these objects. Combining osteomorphology studies and amino acid variations identified by proteomics, one of the retouchers was potentially identified as belonging to the Ursus spelaeus species.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:31:35.234.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	BRAY FABRICE
SpeciesList	scientific name: Mammalia; NCBI TaxID: 40674;
ModificationList	monohydroxylated residue; deaminated residue; iodoacetamide derivatized residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2022-02-01 04:55:59	ID requested
1	2022-06-29 01:37:19	announced
⏵ 2	2023-11-14 08:31:35	announced	2023-11-14: Updated project metadata. 2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: PLEISTOCENE,PALAEOPROTEOMICS, AMINO ACIDS SUBSTITUTION, SCLADINA CAVE, MASS SPECTROMETRY, PEPTIDES MODIFICATIONS, MAMMALIAN BONES, TAXONOMY

Fabrice Bray
contact affiliation	MSAP, UAR 3290, CNRS 59655 villeneuve d'Ascq, France
contact email	fabrice.bray@univ-lille.fr
lab head
BRAY FABRICE
contact affiliation	MSAP USR 3290
contact email	fabrice.bray@univ-lille.fr
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/2022/06/PXD031386

PRIDE project URI

• PRIDE
  1. PXD031386
     1. Label: PRIDE project
     2. Name: Extinct species identification from late Middle Pleistocene and earlier Upper Pleistocene bone fragments and tools not recognizable from their osteomorphological study by an enhanced proteomics protocol