PXD041930

PXD041930 is an original dataset announced via ProteomeXchange.

Title	29 million years of diverse mammalian proteomes recovered from the East African Rift System
Description	Here, we sample small proteomes from the interior enamel of 10 fossils deposited at seven paleontological sites between 1.5 and 29 Ma in the Turkana Basin, a region of northern Kenya in the East African Rift System. We find enamel protein fragments in all fossil specimens including a 29 Ma Arsinoitherium from Topernawi, belonging to a now extinct mammalian order. Identified proteins include the classical structural enamel proteins amelogenin, enamelin, and ameloblastin, but also uncommon enamel proteins including collagens and proteases. Protein fragment abundance and average length decline in progressively older fossils, but we observe significant variability in Early Miocene preservation from site to site, with proboscidean fossils from 16 Ma Buluk preserving substantially more proteins than Rhinocerotidae and Anthracotheriidae fossils from the marginally older Locherangan (18 Ma) and Hippopotamidae from the younger site of Napudet (c. 5-11 Ma). Most specimens yield known clade-specific diagenetiforms that support field taxonomic identifications, with the notable exception of the Arsinoitherium that is without living relatives. Consensus phylogenetic trees suggest the potential for paleoproteomics in supporting taxonomic identifications and resolving evolutionary relationships of extinct taxa but should be approached with caution due to sometimes sparse fragment identification and the potential for sequence diagenesis. We identify numerous likely modifications that support the ancient age of these proteins, and the oldest examples of advanced glycation end-products and carbamylation yet known. The persistence of protein sequences within dense enamel tissues in one of the persistently warmest places on Earth promises the discovery of far older proteomes that will aid in the study of the biology and evolutionary relationships of extinct taxa.
HostingRepository	MassIVE
AnnounceDate	2025-04-30
AnnouncementXML	Submission_2025-04-30_07:27:23.409.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Timothy Cleland
SpeciesList	scientific name: Palaeoloxodon recki; scientific name: Archaeopotamus; scientific name: Hippopotamidae indet.; scientific name: Prodeinotherium hobleyi; scientific name: Zygolophodon sp.; scientific name: Gomphotheriidae indet.; scientific name: Brachyodus aequatorialis; scientific name: Rhinocerotidae indet.; scientific name: Chilotheridium; scientific name: Arsinoitheriidae indet.;
ModificationList	Carbamyl; Carboxymethyl
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-02 08:38:36	ID requested
⏵ 1	2025-04-30 07:27:23	announced

no publication

submitter keyword: paleoproteomics, enamel, amelogenin, ameloblastin

Timothy Cleland
contact affiliation	Smithsonian Institution
contact email	clelandtp@si.edu
lab head
Timothy Cleland
contact affiliation	Smithsonian Institution
contact email	clelandtp@si.edu
dataset submitter

MassIVE dataset URI

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