PXD054549

PXD054549 is an original dataset announced via ProteomeXchange.

Title	Micro-destructive palaeoproteomic analysis of dental enamel from 23 Homo naledi specimens shows no evidence of conventional biological male markers
Description	Understanding intraspecific variation within the hominin fossil record is important and challenging. The limited number and condition of fossils we recover from the Pleistocene compounds this challenge. Unusually, the Rising Star Cave system excavations resulted in a high number of well-preserved specimens of Homo naledi, making this species suitable for an in-depth analysis of variation. The evident lack of intraspecific morphological variation in H. naledi is puzzling, and recently Delezene et al. (2024) showed that the dental morphology observed within the H. naledi collection is compatible with a single sex population. Here we report the mass spectrometric (MS) sequencing of enamel proteomes from twenty-three ca. 335 thousand year old (Ka) dental specimens morphologically attributed to H. naledi. We demonstrate that protein recoveries, when sampling Pleistocene specimens via a minimally-destructive etching method or via the conventional destructive one, are similarly effective. All 23 H. naledi individuals lack confidently identified AMELY specific peptides used to recognise male individuals. By using a semi-quantitative approach, we also show that the lack of AMELY detection is not due to the sensitivity limits of the MS instrument used. Finally, the short enamel proteome sequences reconstructed so far show no variation among the analysed H. naledi individuals and, compared to extinct and extant hominins, there is a substituted position in AMELX. This study demonstrates the feasibility of recovering enamel proteins from Middle Pleistocene specimens via a minimally destructive method that in the future could also be used as a first screening approach to survey ancient protein content and to determine sex.
HostingRepository	PRIDE
AnnounceDate	2026-06-29
AnnouncementXML	Submission_2026-06-29_04:34:09.433.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Palesa Madupe
SpeciesList	scientific name: Homininae; NCBI TaxID: NEWT:207598;
ModificationList	L-ornithine (Arg); L-kynurenine; phosphorylated residue; monohydroxylated residue; deamidated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-02 19:23:55	ID requested
⏵ 1	2026-06-29 04:34:09	announced

10.1016/J.CELL.2026.05.044;

submitter keyword: Homo naledi, Amelogenin,Palaeoproteomics, Enamel

Jesper Velgaard
contact affiliation	Professor at the University of Copenhagen and Deputy Head of Novo Nordisk Foundation Center for Protein Research (CPR) at University of Copenhagen.
contact email	jesper.olsen@cpr.ku.dk
lab head
Palesa Madupe
contact affiliation	University of Copenhagen
contact email	palesa.madupe@palaeoproteomics.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD054549
     1. Label: PRIDE project
     2. Name: Micro-destructive palaeoproteomic analysis of dental enamel from 23 Homo naledi specimens shows no evidence of conventional biological male markers