PXD020516

PXD020516 is an original dataset announced via ProteomeXchange.

Title	Proteome variation with collagen yield in ancient bone
Description	Isotope analyses are some of the most common analytical methods applied to ancient bone, aiding the interpretation of past diets and chronology. For this, the evaluation of “collagen” yield is a routine step that allows for the selection of the specimens that are adequate for subsequent analyses, and samples with below ~1% yield normally discarded. Additionally, during the “collagen extraction” procedure, several sample fractions are generated and subsequently discarded but could contain proteins of analytical interest. In this study we evaluated the proteome variability of different fractions generated during the “collagen extraction” process of 29 samples, and their correlation with the collagen yield. We found that these fractions contained a significant amount of both collagenous and non-collagenous protein (NCP) spectra and that these were not correlated with the collagen yield. The variety of the extracted NCPs was comparable with that normally obtained from ancient samples, and the information obtained can be used to conduct species identification, phylogenetic studies, isotopic analyses and may be used to perform radiocarbon dating on the specimens. Overall, these findings suggest that not only is there value in retaining the fractions typically discarded as waste, but that low collagen yield specimens can still yield useful information.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:18:40.596.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD020516
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Noemi Procopio
SpeciesList	scientific name: Cervus elaphus (Red deer); NCBI TaxID: 9860; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Equus caballus (Horse); NCBI TaxID: 9796;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-22 22:50:42	ID requested
1	2021-02-07 23:31:16	announced
⏵ 2	2024-10-22 05:18:41	announced	2024-10-22: Updated project metadata.

10.6019/PXD020516;

Procopio N, Hopkins RJA, Harvey VL, Buckley M, Proteome Variation with Collagen Yield in Ancient Bone. J Proteome Res, 20(3):1754-1769(2021) [pubmed]

10.1021/acs.jproteome.0c01014;

submitter keyword: Proteomics

ancient bone

collagen

NCPs

radiocarbon dating

stable isotopes.

Michael Buckley
contact affiliation	Manchester Institute of Biotechnology, 131 Princess Street, The University of Manchester, Manchester, M1 7DN, UK
contact email	m.buckley@manchester.ac.uk
lab head
Noemi Procopio
contact affiliation	University of Central Lancashire
contact email	noemi.procopio@northumbria.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD020516
     1. Label: PRIDE project
     2. Name: Proteome variation with collagen yield in ancient bone