PXD062254

PXD062254 is an original dataset announced via ProteomeXchange.

Title	Deep palaeoproteomic profiling of archaeological human brains
Description	Palaeoproteomics leverages the persistence, diversity, and biological import of ancient proteins to explore the past, and answer fundamental questions about phylogeny, environment, diet, and disease. These insights are largely gleaned from hard tissues like bone and teeth, as well-established protocols exist for extracting ancient proteins from mineralised tissues. No such method, however, exists for the soft tissues, which are underexplored in palaeoproteomics given permission for destructive analysis routinely depends on a proven methodology. Considering less than one-tenth of all human proteins are expressed in bone, compared to three-quarters in the internal organs, the amount of biological information presently inaccessible is substantial. We address this omission with an optimised LC-FAIMS-MS/MS workflow yielding the largest, most diverse palaeoproteome yet described. Using archaeological human brains, we test ten protocols with varied chemistries and find that urea lysis effectively disrupts preserved membrane regions to expose low-abundant, intracellular analytes. Further, we show that ion mobility spectrometry improves unique protein identification by as much as 40%, and represents a means of “pre-cleaning” dirty archaeological samples. Our methodology will be useful for improving protein recovery from a range of ancient tissues and depositional environments.
HostingRepository	PRIDE
AnnounceDate	2025-04-29
AnnouncementXML	Submission_2025-04-29_06:13:32.771.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alexandra Morton-Hayward
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-26 03:23:22	ID requested
⏵ 1	2025-04-29 06:13:33	announced

Dataset with its publication pending

submitter keyword: brain

palaeoproteomics

LC-MS/MS

ion mobility

FAIMS

Roman Fischer
contact affiliation	Associate Professor and Head of Discovery Proteomics Facility
contact email	roman.fischer@ndm.ox.ac.uk
lab head
Alexandra Morton-Hayward
contact affiliation	University of Oxford
contact email	alexandra.morton-hayward@earth.ox.ac.uk
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/PXD062254

PRIDE project URI

• PRIDE
  1. PXD062254
     1. Label: PRIDE project
     2. Name: Deep palaeoproteomic profiling of archaeological human brains