PXD023399

PXD023399 is an original dataset announced via ProteomeXchange.

Title	Palmer et al: Dental Method Comparison
Description	The dental calculus proteome from human remains is a considered a valuable archaeological resource for studying the diet, oral microbiome, health/disease of individuals and occupation activities individuals within past societies/civilisations. The combination of advancements in LC/MS instrument sensitivity and sample prepartion methods enables the analysis of these well preserved proteomes otherwise invisible to other biomolecular approaches. Maximizing proteome recovery from this minute and finite resource is paramount to our understanding of these past societies and civilisations in terms of diet and disease. Here we compare the more traditional ultrafiltration-based and acetone precipitation approaches with the newer paramagnetic bead approach (SP3) in a step towards achieving this aim. We specifically evaluate different acids (EDTA and HCl) and proteome extraction methodologies (Ultrafiltration, Acetone Precipitation and SP3)to test the influence of demineralization acid and method of extraction on the recovered proteome complexity (including numbers of peptides recovered) and sequence coverageand observed for these ancient dental calculus specimens.
HostingRepository	PRIDE
AnnounceDate	2021-02-19
AnnouncementXML	Submission_2021-02-18_23:43:55.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karren Palmer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-04 04:00:45	ID requested
⏵ 1	2021-02-18 23:43:56	announced

Palmer KS, Makarewicz CA, Tishkin AA, Tur SS, Chunag A, Diimajav E, Jamsranjav B, Buckley M, Comparing the Use of Magnetic Beads with Ultrafiltration for Ancient Dental Calculus Proteomics. J Proteome Res, 20(3):1689-1704(2021) [pubmed]

submitter keyword: Dental calculus proteome, EDTA, HCl, Acetone precipitation, Archaeologica dairy proteinl, SP3, Ultrafiltration, Deamidation, Orbi-trap, QE, Mass Spectrometry, Beta-lactoglobulin, Casein

Michael Buckley
contact affiliation	School of Natural Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K.
contact email	M.Buckley@manchester.ac.uk
lab head
Karren Palmer
contact affiliation	University of Manchester
contact email	Karren.Palmer@manchester.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/2021/02/PXD023399

PRIDE project URI

• PRIDE
  1. PXD023399
     1. Label: PRIDE project
     2. Name: Palmer et al: Dental Method Comparison