What's the catch? Archaeological application of rapid collagen-based species identification for Pacific Salmon

Richter, Kristine Korzow; McGrath, Krista; Masson-MacLean, Édouard; Hickinbotham, Simon; Tedder, Andrew; Britton, Kate; Bottomley, Zoe; Dobney, Keith; Hulme-Beaman, Ardern; Zona, Margherita; Fischer, Román; Collins, Matthew J.; Speller, Camilla

doi:10.1016/j.jas.2020.105116

Cited by 24 publications

(19 citation statements)

References 104 publications

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“…The peaks at m/z 1550 and m/z 2553 did not always appear or show high intensity in the modern wild bovid spectra. It is a well-reported phenomenon that certain peptides are ‘poor flyers’ in MALDI-TOF 43 . We therefore decided to investigate only the peak at m/z 1532 further, since it was present in all three wild bovids (Fig.…”

Section: Resultsmentioning

confidence: 99%

Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP

Coutu

Taurozzi

Mackie

et al. 2021

Sci Rep

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We used palaeoproteomics and peptide mass fingerprinting to obtain secure species identifications of key specimens of early domesticated fauna from South Africa, dating to ca. 2000 BP. It can be difficult to distinguish fragmentary remains of early domesticates (sheep) from similar-sized local wild bovids (grey duiker, grey rhebok, springbok—southern Africa lacks wild sheep) based on morphology alone. Our analysis revealed a Zooarchaeology by Mass Spectrometry (ZooMS) marker (m/z 1532) present in wild bovids and we demonstrate through LC–MS/MS that it is capable of discriminating between wild bovids and caprine domesticates. We confirm that the Spoegrivier specimen dated to 2105 ± 65 BP is indeed a sheep. This is the earliest directly dated evidence of domesticated animals in southern Africa. As well as the traditional method of analysing bone fragments, we show the utility of minimally destructive sampling methods such as PVC eraser and polishing films for successful ZooMS identification. We also show that collagen extracted more than 25 years ago for the purpose of radiocarbon dating can yield successful ZooMS identification. Our study demonstrates the importance of developing appropriate regional frameworks of comparison for future research using ZooMS as a method of biomolecular species identification.

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Section: Resultsmentioning

confidence: 99%

Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP

Coutu

Taurozzi

Mackie

et al. 2021

Sci Rep

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“…It is also fast and inexpensive, which allows it to be performed at scale and with high throughput. This combination of features makes it a highly flexible method that can successfully support both small-scale budget-restricted projects on specific questions , as well as large-scale exploratory studies of thousands of samples. , …”

Section: Ancient Proteinsmentioning

confidence: 99%

“…In phylogenetic studies of taxa for which the exact protein sequence is unknown, software is available for de novo sequencing . This is especially valuable for determining sequences in extinct species for which genomic data cannot be obtained ,,, or authenticating PMF markers. ,, A variety of software has been used to perform de novo sequencing on ancient proteins, including PEAKS, Byonic, and MaxNovo. Algorithmic differences between the different software influence the accuracy of identification.…”

Section: Ancient Proteinsmentioning

confidence: 99%

“…ZooMS identification using MALDI-TOF is performed using a database of taxonomically informative marker peaks, and it is important that the sequences of newly developed markers are first verified as authentic collagen sequences with taxonomically informative amino acid substitutions using MALDI-TOF/TOF or LC–MS/MS, , although there are cases where this has not been feasible. , Large mammals, particularly European species, make up a large proportion of the published markers, e.g., ,, but markers for other taxonomic groups are increasingly being developed, including for non-European large mammals, ,,− rodents, , bats, cetaceans, , marsupials, birds, , fish, ,, amphibians, and reptiles. ,,, …”

Section: Applications In Paleoproteomicsmentioning

confidence: 99%

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Paleoproteomics

2022

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Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human−animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

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“…The identification and confirmation of peptide biomarkers were performed following the methodology described in Richter et al . [ 60 ]. MALDI spectra were visually inspected with FlexAnalysis v. 3.4 (Bruker Daltonics) and compared to a list of published peptide markers for Australian marsupials [ 53 ].…”

Section: Methodsmentioning

confidence: 99%

Species identification of Australian marsupials using collagen fingerprinting

et al. 2021

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The study of faunal remains from archaeological sites is often complicated by the presence of large numbers of highly fragmented, morphologically unidentifiable bones. In Australia, this is the combined result of harsh preservation conditions and frequent scavenging by marsupial carnivores. The collagen fingerprinting method known as zooarchaeology by mass spectrometry (ZooMS) offers a means to address these challenges and improve identification rates of fragmented bones. Here, we present novel ZooMS peptide markers for 24 extant marsupial and monotreme species that allow for genus-level distinctions between these species. We demonstrate the utility of these new peptide markers by using them to taxonomically identify bone fragments from a nineteenth-century colonial-era pearlshell fishery at Bandicoot Bay, Barrow Island. The suite of peptide biomarkers presented in this study, which focus on a range of ecologically and culturally important species, have the potential to significantly amplify the zooarchaeological and paleontological record of Australia.

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What's the catch? Archaeological application of rapid collagen-based species identification for Pacific Salmon

Cited by 24 publications

References 104 publications

Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP

Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP

Paleoproteomics

Species identification of Australian marsupials using collagen fingerprinting

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