PXD001411

PXD001411 is an original dataset announced via ProteomeXchange.

Title	Ancient proteins resolve the evolutionary history of Darwin's South American ungulates
Description	The project aimed to characterize the collagen type I (COL1) sequences from Pleistocene Macrauchenia sp. and Toxodon sp. bone samples, and by comparison with existing COL1 sequences available from genomic sources establish the phylogenetic position of both extinct species. In order to resolve their phylogenetic position, COL1 was extracted from two Toxodon (samples MLP201204, MACN201212, York12, York13) and two Macrauchenia (samples MLP201212, MACN201202, York14, York15). In addition, modern and Pleistocene COL1 was extracted from additional species currently not present in available databases (Mylodon darwinii, Cyclopes didactylus, Hippopotamus amphibius, Tapirus terrestris) or from species for which COL1 sequences are available (Equus sp., Oryceropus afer). All extractions were performed at BioArCh, University of York (UK). Analyses took place on Bruker maXis HD (Macrauchenia sp., Toxodon sp., Equus sp.) and Thermo Scientific Hybrid Quadruopole-Orbitrap (Macrauchenia sp., Toxodon sp., Mylodon darwinii, Cyclopes didactylus, Hippopotamus amphibius, Tapirus terrestris, Oryceropus afer) platforms.
HostingRepository	PRIDE
AnnounceDate	2015-03-19
AnnouncementXML	Submission_2015-05-27_06:48:59.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Frido Welker
SpeciesList	scientific name: Equus; NCBI TaxID: 35510; scientific name: Orycteropus afer (Aardvark); NCBI TaxID: 9818; scientific name: Cyclopes didactylus (Silky anteater) (Myrmecophaga didactyla); NCBI TaxID: 84074; scientific name: Mylodon darwinii (Giant ground sloth); NCBI TaxID: 48784; scientific name: Tapirus terrestris (Lowland tapir) (Brazilian tapir); NCBI TaxID: 9801; scientific name: unidentified; NCBI TaxID: 32644; scientific name: Hippopotamus amphibius (Hippopotamus); NCBI TaxID: 9833;
ModificationList	hydroxylated lysine; deamidated residue; monohydroxylated residue; monohydroxylated proline
Instrument	Q Exactive; LTQ Orbitrap Velos; maXis

Revision	Datetime	Status	ChangeLog Entry
0	2014-10-20 01:15:59	ID requested
1	2015-03-19 04:16:41	announced
⏵ 2	2015-05-27 06:49:00	announced	Updated publication reference for PubMed record(s): 25799987.

Welker F, Collins MJ, Thomas JA, Wadsley M, Brace S, Cappellini E, Turvey ST, Reguero M, Gelfo JN, Kramarz A, Burger J, Thomas-Oates J, Ashford DA, Ashton PD, Rowsell K, Porter DM, Kessler B, Fischer R, Baessmann C, Kaspar S, Olsen JV, Kiley P, Elliott JA, Kelstrup CD, Mullin V, Hofreiter M, Willerslev E, Hublin JJ, Orlando L, Barnes I, MacPhee RD, Ancient proteins resolve the evolutionary history of Darwin's South American ungulates. Nature, 522(7554):81-4(2015) [pubmed]

curator keyword: Biological

submitter keyword: LC-MS/MS, Macrauchenia, Toxodon, Bruker maXis HD, Thermo Scientific Hybrid Quadrupole-Orbitrap, de novo collagen sequencing, Pleistocene

Matthew Collins
contact affiliation	BioArCh, University of York, United Kingdom
contact email	matthew.collins@york.ac.uk
lab head
Frido Welker
contact affiliation	PhD candidate: Department of Human Evolution, MPI-EVA. Associate Researcher: BioArCh, Department of Archaeology, University of York
contact email	frido.welker@palaeo.eu
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/2015/03/PXD001411

PRIDE project URI

• PRIDE
  1. PXD001411
     1. Label: PRIDE project
     2. Name: Ancient proteins resolve the evolutionary history of Darwin's South American ungulates