PXD000412-3

PXD000412 is an original dataset announced via ProteomeXchange.

Title	Human dental calculus LC-MS/MS
Description	The 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.
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2015-03-18_02:56:50.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000412
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christina Warinner
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Ovis; NCBI TaxID: 9935; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	deamidated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deaminated residue
Instrument	LTQ Orbitrap Velos; Q Exactive; maXis

Revision	Datetime	Status	ChangeLog Entry
0	2013-08-14 03:03:45	ID requested
1	2014-01-29 03:39:13	announced
2	2014-07-24 05:16:41	announced	Updated project metadata.
⏵ 3	2015-03-18 02:56:51	announced	Updated project metadata.
4	2017-06-20 05:42:37	announced	Updated project metadata.
5	2017-10-24 00:06:40	announced	Updated project metadata.

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]

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

Christina G Warinner
contact affiliation	Department of Anthropology, University of Oklahoma, USA
contact email	twarinner@gmail.com
lab head
Christina Warinner
contact affiliation	Centre for Evolutionary Medicine (ZEM)
contact email	twarinner@gmail.com
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/2014/01/PXD000412

PRIDE project URI

• PRIDE
  1. PXD000412
     1. Label: PRIDE project
     2. Name: Human dental calculus LC-MS/MS