PXD022878

PXD022878 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Examining collagen preservation through glutamine deamidation at Denisova Cave
Description	Samples were used for a study on the ability to use deamidation rates to assess relative chronology at Denisova Cave. The majority of the samples for the study were analyzed using peptide mass fingerprinting (data publicly available - see associated manuscript for details). 15 samples from 7 layers in Denisova Cave were chosen for LC-MS/MS analysis. Prior to analysis samples were demineralized in hydrochloric acid, gelatinized in ammonium bicarbonate, digested with trypsin, and desalted with C18 ZipTips. Data was processed using Byonic with SwissProt as the database to obtain a focused database of just the proteins present in the samples. This focused database was combined with curated collagen sequences (database presented here) and used for analysis with MaxQuant and deamiDATE. For more details see associated publication. Provided here are the raw files, peak lists for Byonic, results files for Byonic, sequence database (focused database and currated collagen sequences), metadata file with information linking the file names here to the file names of the peptide mass fingerprinting samples, and a zip file of the Max Quant and deamiDATE results.
HostingRepository	MassIVE
AnnounceDate	2021-07-22
AnnouncementXML	Submission_2021-07-22_06:55:21.191.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Kristine Korzow Richter
SpeciesList	scientific name: Bos; common name: oxen, cattle; NCBI TaxID: 9903; scientific name: Ursus; NCBI TaxID: 9639; scientific name: Equus; NCBI TaxID: 9789; scientific name: Capra; NCBI TaxID: 9922; scientific name: Ovis; NCBI TaxID: 9935;
ModificationList	Deamidated; Oxidation
Instrument	Q Exactive HF

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-02 18:46:16	ID requested
⏵ 1	2021-07-22 06:55:21	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: collagen, deamidation, archaeology, chronology, relative dating

submitter keyword: collagen, deamidation, archaeology, chronology, relative dating

Contact List

Samantha Brown
contact affiliation	Department of Archaeology, Max-Planck Institute for the Science of Human History
contact email	brown@shh.mpg.de
lab head
Kristine Korzow Richter
contact affiliation	Max Planck Institute for the Science of Human History
contact email	kkrichter@palaeome.org
lab head
Kristine Korzow Richter
contact affiliation	Max Planck Institute for the Science of Human History
contact email	kkrichter@palaeome.org
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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://massive.ucsd.edu/MSV000086548/

MassIVE dataset URI

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://massive.ucsd.edu/MSV000086548/