Peptide mass fingerprinting of preserved collagen in archaeological fish bones for the identification of flatfish in European waters

Abstract

Bones of Pleuronectiformes (flatfish) are often not identified to species due to the lack of diagnostic features on bones that allow adequate distinction between taxa. This hinders in-depth understanding of archaeological fish assemblages and particularly flatfish fisheries throughout history. This is especially true for the North Sea region, where several commercially significant species have been exploited for centuries, yet their archaeological remains continue to be understudied. In this research, eight peptide biomarkers for 18 different species of Pleuronectiformes from European waters are described using MALDI-TOF MS and liquid chromatography tandem mass spectrometry data obtained from modern reference specimens. Bone samples ( n = 202) from three archaeological sites in the UK and France dating to the medieval period ( ca seventh–sixteenth century CE) were analysed using zooarchaeology by mass spectrometry (ZooMS). Of the 201 that produced good quality spectra, 196 were identified as flatfish species, revealing a switch in targeted species through time and indicating that ZooMS offers a more reliable and informative approach for species identification than osteological methods alone. We recommend this approach for future studies of archaeological flatfish remains as the precise species uncovered from a site can tell much about the origin of the fish, where people fished and whether they traded between regions.

Geometric morphometric analysis of Pleuronectiformes vertebrae: A new tool to identify archaeological fish remains?

“…For each sample the most probable family and species were noted as well as the probability score for the classification. The accuracy of GMM on archaeological samples was confirmed by identifying the samples using collagen peptide mass fingerprinting (ZooMS), following Dierickx et al ( 2022 ), where the results of the identifications of the archaeological samples of this study were published.…”

“…Alternative identification methods, such as collagen peptide mass fingerprinting (e.g. Dierickx et al, 2022 ) and DNA (e.g. Kijewska et al, 2009 ; Pappalardo & Ferrito, 2015 ), are still recommended to differentiate between vertebrae of different species of archaeological flatfish in the North Sea area.…”

“…following Dierickx et al (2022), where the results of the identifications of the archaeological samples of this study were published.…”

A photographic atlas for European freshwater and migratory fish remains and key considerations for their analysis

“…Peptide mass fingerprints, which differ between taxonomic groups due to variations in their amino acid sequences, can be compared to modern reference samples to identify the species of the archeological sample (Baker et al, 2023). ZooMS has shown great utility for identifying archeological fish remains, allowing separation of closely related species and identification from highly fragmented remains or elements lacking diagnostic features (Buckley et al, 2021(Buckley et al, , 2022Dierickx et al, 2022;Harvey et al, 2018Harvey et al, , 2022Richter et al, 2011Richter et al, , 2020Rick et al, 2019). Fish may also represent a challenge for ZooMS due to their taxonomic diversity (Baker et al, 2023), although the range of fish species represented in reference databases continues to increase.…”

COL1A2 Barcoding: Bone Species Identification via Shotgun Proteomics

“…A species identification method for such fragmentary bones that has recently attracted significant interest is the use of interspecific sequence differences in bone collagen proteins. − Collagen is very abundant and stable in bone and is reported to be recoverable from even very old bones. , Furthermore, compared with DNA, collagen is insoluble in water and oil, so contaminants can be washed off, and because collagen proteins have some degree of tissue specificity, it is possible to narrow down the tissue source from which the species identification result was obtained. The most popular of these collagen-based methods is collagen peptide mass fingerprinting, known as zooarcheology by mass spectrometry (ZooMS). ,, This method identifies bone species by detecting species marker peptides produced by trypsin digestion of collagen using matrix-assisted laser desorption/ionization (MALDI) MS. Because it is a very high-throughput method, large numbers of bone samples can be processed. , Although the development of ZooMS peptide markers has focused mainly on mammals, ,− they have also been developed for other vertebrates, including birds, , reptiles, amphibians, and fish. − With the advent of ZooMS, it became possible to extract species information from even extremely degraded and fragmented bone samples, which had been previously thought to be utterly impossible. Currently, ZooMS is used primarily in archeology and paleontology, but it is beginning to be used in forensic science, and its use is steadily growing.…”