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PXD023399 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePalmer et al: Dental Method Comparison
DescriptionThe 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterKarren Palmer
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
InstrumentQ Exactive; LTQ Orbitrap Elite
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-01-04 04:00:45ID requested
12021-02-18 23:43:56announced
Publication List
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]
Keyword List
submitter keyword: Dental calculus proteome, EDTA, HCl, Acetone precipitation, Archaeologica dairy proteinl, SP3, Ultrafiltration, Deamidation, Orbi-trap, QE, Mass Spectrometry, Beta-lactoglobulin, Casein
Contact List
Michael Buckley
contact affiliationSchool of Natural Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K.
contact emailM.Buckley@manchester.ac.uk
lab head
Karren Palmer
contact affiliationUniversity of Manchester
contact emailKarren.Palmer@manchester.ac.uk
dataset submitter
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Dataset FTP location
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