PXD024487 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2022-05-20 |
AnnouncementXML | Submission_2022-05-19_16:30:21.140.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Patrick Ruether |
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 |
Dataset History
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. |
Publication List
Keyword List
submitter keyword: Species identification, DDA, DIA, Orbitrap Exploris 480, Evosep, Palaeoproteomics |
Contact List
Jesper Velgaard Olsen |
contact affiliation | Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark |
contact email | jesper.olsen@cpr.ku.dk |
lab head | |
Patrick Ruether |
contact affiliation | NNF Center for Protein Research - University of Copenhagen |
contact email | patrick.ruether@cpr.ku.dk |
dataset submitter | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD024487
- Label: PRIDE project
- Name: SPIN - Species by Proteome INvestigation