PXD052635

PXD052635 is an original dataset announced via ProteomeXchange.

Title	An early Miocene enamel proteome from an early diverging rhinocerotid
Description	The evolutionary history of Rhinocerotidae has been the subject of significant debate among palaeontologists, with several paradigm shifts within the last quarter century, typically centered around a speculated deep-basal split between Rhinocerotinae and Elasmotheriinae. Here, we recover an endogenous ancient enamel proteome from an Early Miocene (20+Ma) old rhinocerotid from the Haughton Formation of Canada’s High Arctic. Ancient proteomes sufficient for phylogenetic analysis have not previously been recovered from beyond the Pliocene, making it difficult to reconstruct the evolutionary relationships and divergence times of fossil taxa that are beyond the reach of ancient DNA. Here, phylogenetic analysis of our proteomic data suggests the split between Elasmotheriinae and Rhinocerotinae occurred much later than previously speculated, in the late Eocene or Oligocene. The authenticity of ancient the ancient proteome is supported by a suite of post-translational modifications associated with advanced degradation, including a significant degree of arginine->ornithine conversion and high rates of advanced forms of tryptophan and histidine oxidation.
HostingRepository	PRIDE
AnnounceDate	2025-07-06
AnnouncementXML	Submission_2025-07-06_06:48:38.018.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ryan Sinclair Paterson
SpeciesList	scientific name: Rhinocerotidae; NCBI TaxID: 9803;
ModificationList	dihydroxylated residue; phosphorylated residue; monohydroxylated residue; deamidated residue
Instrument	Q Exactive HF; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-28 08:05:28	ID requested
⏵ 1	2025-07-06 06:48:38	announced

10.1038/S41586-025-09231-4;

submitter keyword: Rhinocerotidae, enamel, LC-MS/MS

Enrico Cappellini
contact affiliation	Globe Institute, University of Copenhagen, Denmark
contact email	enrico.cappellini@sund.ku.dk
lab head
Ryan Sinclair Paterson
contact affiliation	University of Copenhagen
contact email	ryan.sinclair@palaeoproteomics.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD052635
     1. Label: PRIDE project
     2. Name: An early Miocene enamel proteome from an early diverging rhinocerotid