PXD022368-1

PXD022368 is an original dataset announced via ProteomeXchange.

Title	Milking it? Assessing the degradation of ancient milk proteomes
Description	The origins, prevalence and nature of dairying have been long debated by archaeologists. Within the last decade, new advances in high-resolution mass spectrometry have allowed for the direct detection of milk proteins from archaeological remains, including ceramics, dental calculus, and preserved dairy products. Proteins recovered from archaeological remains are susceptible to post-excavation and laboratory contamination, a particular concern for ancient dairying studies as milk proteins are potential laboratory contaminants. Here, we examine how site-specific rates of deamidation can be used to elucidate patterns of peptide degradation, and authenticate ancient milk proteins. First, we characterize site-specific deamidation patterns in modern milk products and experimental samples, confirming that deamidation occurs primarily at low half-time sites. We then compare this to previously published ancient proteomic data from six studies reporting ancient milk peptides. We confirm that site-specific deamidation rates, on average, are more advanced in beta-lactoglobulin recovered from ancient dental calculus and pottery residues. Nevertheless, deamidation rates displayed a high degree of variability, making it challenging to authenticate samples with relatively few milk peptides. We demonstrate that site-specific deamidation is a useful tool for identifying modern contamination but highlight the need for multiple lines of evidence to authenticate ancient protein data.
HostingRepository	PRIDE
AnnounceDate	2021-08-05
AnnouncementXML	Submission_2021-08-05_02:48:03.512.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Abigail Ramsøe
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidoethyl-L-cysteine; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-05 00:45:25	ID requested
⏵ 1	2021-08-05 02:48:03	announced
2	2021-08-06 01:01:17	announced	2021-08-06: Updated project metadata.

10.1038/S41598-021-87125-X;

submitter keyword: palaeoproteomics, milk, authentication, deamidation

Matthew Collins
contact affiliation	The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
contact email	matthew@palaeome.org
lab head
Abigail Ramsøe
contact affiliation	Geogenetics, UCPH
contact email	abigail.ramsoe@sund.ku.dk
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/2021/08/PXD022368

PRIDE project URI

• PRIDE
  1. PXD022368
     1. Label: PRIDE project
     2. Name: Milking it? Assessing the degradation of ancient milk proteomes