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PXD000412-3

PXD000412 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleHuman dental calculus LC-MS/MS
DescriptionThe purpose of this study was to investigate oral microbiome and host proteins in archaeological human dental tissues using a shotgun proteomics approach. The research focuses on dental calculus (mineralized plaque), dentine, a carious lesion, and an alveolar bone abscess from the medieval site of Dalheim, Germany (ca. AD 950-1200). For comparison, proteins were also analyzed from archaeological faunal dental tissues and human dental calculus samples from modern Swiss dental patient controls. Protein extraction and generation of tryptic peptides from tooth and dental calculus specimens was performed using a filter-aided sample preparation (FASP) protocol, modified for mineralized and degraded samples. Total protein extraction was performed on a total of fourteen samples: four ancient human calculus samples (indicated as: G12, B71, B61, and B78), four ancient human tooth root samples (indicated as: G12, B17, B61, and B78), one carious lesion (indicated as: B17), one alveolar bone abscess (indicated as: B17), two ancient fauna crown cementum/calculus samples (indicated as: F1 [sheep] and F5 [cattle]), and two modern dental calculus samples from clinical patients (indicated as: P1 and P2). All samples were extracted at the Centre for Evolutionary Medicine (ZEM) at the University of Zürich with the exception of dental calculus from G12, P1, and P2, which were extracted at the Center for GeoGenetics (CGG) at the University of Copenhagen. Two samples (G12 and B61 calculus) were extracted a second time in an independent laboratory at the University of York (YORK) for comparison. Sample extracts were then sequenced (LC-MS/MS) at the Functional Genomics Center Zürich (FGCZ) using an LTQ-Orbitrap Velos, at the Novo Nordisk Foundation Center for Protein Research (CPR) using a Q-Exactive Hybrid Quadrupole Orbitrap, and at the University of York’s Proteomics and Analytical Biochemistry Laboratories (PABL) using a MaXis UHR-Qq-TOF.
HostingRepositoryPRIDE
AnnounceDate2014-07-24
AnnouncementXMLSubmission_2015-03-18_02:56:50.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD000412
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterChristina Warinner
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Ovis; NCBI TaxID: 9935; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationListdeamidated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deaminated residue
InstrumentLTQ Orbitrap Velos; Q Exactive; maXis
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-08-14 03:03:45ID requested
12014-01-29 03:39:13announced
22014-07-24 05:16:41announcedUpdated project metadata.
32015-03-18 02:56:51announcedUpdated project metadata.
42017-06-20 05:42:37announcedUpdated project metadata.
52017-10-24 00:06:40announcedUpdated project metadata.
Publication List
Warinner C, Rodrigues JF, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-Garc, í, a DC, Eppler E, Seiler R, Hansen LH, Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup CD, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis CM, Collins MJ, Gilbert MT, R, ü, hli F, Cappellini E, Pathogens and host immunity in the ancient human oral cavity. Nat Genet, 46(4):336-44(2014) [pubmed]
Keyword List
curator keyword: Biomedical
submitter keyword: Human, sheep, cattle, dental plaque, dental calculus, dentine, cementum, bone, abscess, caries, periodontitis, archaeological, medieval, LTQ-Orbitrap Velos, Q-Exactive Hybrid Quadrupole Orbitrap, maXis UHR-Qq-TOF
Contact List
Christina G Warinner
contact affiliationDepartment of Anthropology, University of Oklahoma, USA
contact emailtwarinner@gmail.com
lab head
Christina Warinner
contact affiliationCentre for Evolutionary Medicine (ZEM)
contact emailtwarinner@gmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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