PXD001827

PXD001827 is an original dataset announced via ProteomeXchange.

Title	Extinct Bison Latifrons Proteomics
Description	Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado and processed for proteomics analysis. The specimens come from Pleistocene megafauna, Bison latifrons, dating back to 110 or 120 ka. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to collagen I. In addition, we analyzed a specimen from the extinct Bison latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of post-translational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified. Meta-analyses of data from other studies indicates that this modification may be enriched in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified. These data provide a framework for analyzing ancient protein signatures in well-preserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation.
HostingRepository	PRIDE
AnnounceDate	2015-07-17
AnnouncementXML	Submission_2015-07-16_21:21:40.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD001827
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Matthew Wither
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	Oxidation; Deamidated
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-02-19 06:31:20	ID requested
⏵ 1	2015-07-16 21:21:41	announced

Hill RC, Wither MJ, Nemkov T, Barrett A, D'Alessandro A, Dzieciatkowska M, Hansen KC, Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry

Hydroxylysine Glycosides are a Common Feature of Ancient Collagen. Mol Cell Proteomics, 14(7):1946-58(2015) [pubmed]

curator keyword: Biological

submitter keyword: Bison latifrons, LC-MS/MS, Paleoproteomics, Hydroxylysine glycosylation, Snowmass, Ziegler Reservoir

Kirk Charles Hansen
contact affiliation	Dept. of Biochemistry and Molecular Genetics, University of Colorado-Denver: Anschutz Medical Campus, Aurora, CO
contact email	kirk.hansen@ucdenver.edu
lab head
Matthew Wither
contact affiliation	University of Colorado Denver
contact email	matthew.wither@ucdenver.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001827
     1. Label: PRIDE project
     2. Name: Extinct Bison Latifrons Proteomics