PXD010041

PXD010041 is an original dataset announced via ProteomeXchange.

Title	Species identification of ancient Lithuanian fish remains using collagen fingerprinting
Description	Morphological identification of ancient bone is often problematic due to heavy fragmentation that generally influences zooarchaeological assemblages. Fish bones are more taphonomically sensitive than those of other vertebrates as they are typically smaller and less biomineralised. Thus, taxonomic identification based on the preservation of morphological features is often extremely limited and can reduce or eliminate the usefulness of an assemblage for inferring taxon information. Currently, one of the most time- and cost-efficient methods of achieving faunal identity from ancient bone is by the collagen fingerprinting technique known as ZooMS (Zooarchaeology by Mass Spectrometry). ZooMS harnesses the potential of preserved collagen, which is the most dominant and time-stable protein in bone. In this research, ZooMS is applied to ancient Baltic region fish assemblages that are between 500 and 6000 years old in order to define species identity and construct assemblage compositions. Alongside inferences into environmental and biological shifts from the Neolithic era to present day in the Baltic region, we demonstrate for the first time the ability to distinguish between recently diverged members of the Salmo (salmon) and Scophthalmus (turbot) genera. ZooMS analysis highlights 7% of the collagen-containing assemblage as having been morphologically identified incorrectly and has facilitated taxonomic refinement of a further 28% of samples, including some of the morphologically indeterminate bone fragments. This research emphasises the great potential of ZooMS in identifying ichthyoarchaeological bone remains to species-level, and provides a case for the use of collagen fingerprinting in contributing to baseline fisheries and ecological data, to inform modern management.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_06:56:26.579.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Virginia Harvey
SpeciesList	scientific name: Scophthalmus rhombus; NCBI TaxID: 65125; scientific name: Salmo trutta trutta; NCBI TaxID: 227976; scientific name: Esox lucius; NCBI TaxID: 8010; scientific name: Carassius carassius; NCBI TaxID: 217509; scientific name: Salmo salar (Atlantic salmon); NCBI TaxID: 8030; scientific name: Sander lucioperca; NCBI TaxID: 283035; scientific name: Silurus glanis; NCBI TaxID: 94993; scientific name: Scophthalmus maximus; NCBI TaxID: 52904; scientific name: Salmo trutta fario; NCBI TaxID: 99804; scientific name: Gadus morhua (Atlantic cod); NCBI TaxID: 8049;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite; nanoACQUITY UPLC

Revision	Datetime	Status	ChangeLog Entry
0	2018-06-05 08:25:53	ID requested
1	2018-08-29 06:10:38	announced
2	2019-03-11 14:35:37	announced	Updated publication reference for DOI(s): https://doi.org/10.1016/j.jas.2018.07.006.
⏵ 3	2023-11-14 06:56:26	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Zooarchaeology, ZooMS, ichthyoarchaeology, species identification, Neolithic, collagen fingerprinting, fish bone

Michael Buckley
contact affiliation	School of Earth and Environmental Sciences, The University of Manchester
contact email	m.buckley@manchester.ac.uk
lab head
Virginia Harvey
contact affiliation	University of Manchester
contact email	virginia.harvey@manchester.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD010041
     1. Label: PRIDE project
     2. Name: Species identification of ancient Lithuanian fish remains using collagen fingerprinting