PXD024487

PXD024487 is an original dataset announced via ProteomeXchange.

Title	SPIN - Species by Proteome INvestigation
Description	Species determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce “Species by Proteome INvestigation” (SPIN), a shotgun proteomics workflow capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirmed the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produced reproducible results between replicates, which were consistent with morphological analysis. Finally, we demonstrated the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study was focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.
HostingRepository	PRIDE
AnnounceDate	2023-05-14
AnnouncementXML	Submission_2023-05-14_14:21:57.652.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	PatrickRuether
SpeciesList	scientific name: Pan troglodytes (Chimpanzee); NCBI TaxID: 9598; scientific name: Pongo pygmaeus (Bornean orangutan); NCBI TaxID: 9600; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Equus caballus (Horse); NCBI TaxID: 9796;
ModificationList	N-ethylmaleimide derivatized cysteine; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-03 00:48:09	ID requested
1	2022-05-19 16:30:22	announced
⏵ 2	2023-05-14 14:21:58	announced	2023-05-14: Updated project metadata.

R, ü, ther PL, Husic IM, Bangsgaard P, Gregersen KM, Pantmann P, Carvalho M, Godinho RM, Friedl L, Cascalheira J, Taurozzi AJ, J, ø, rkov MLS, Benedetti MM, Haws J, Bicho N, Welker F, Cappellini E, Olsen JV, SPIN enables high throughput species identification of archaeological bone by proteomics. Nat Commun, 13(1):2458(2022) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: DIA, Orbitrap Exploris 480, Evosep,Species identification, DDA, Palaeoproteomics

Jesper VelgaardOlsen
contact affiliation	Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
contact email	jesper.olsen@cpr.ku.dk
lab head
PatrickRuether
contact affiliation	NNF Center for Protein Research - University of Copenhagen
contact email	patrick.ruether@cpr.ku.dk
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/2022/05/PXD024487

PRIDE project URI

• PRIDE
  1. PXD024487
     1. Label: PRIDE project
     2. Name: SPIN - Species by Proteome INvestigation