ArticleNature communications2022
SPIN enables high throughput species identification of archaeological bone by proteomics.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
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30 citing papers in PubMed, 1 synthesis or guideline pooled it, 78 citations in OpenAlex.
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- Palaeoproteomic Deconvolution of Physical and Genetic Collagen Mixtures.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Ancient DNA as a temporal lens: reconstructing evolution, migration, and disease dynamics.Journal, genetic engineering & biotechnology · 2026Review
- MARLOWE: taxonomic characterization of unknown samples for forensics using de novo peptide identification.Scientific reports · 2026Article
- Assessing the Potential of Ancient Protein Sequences in the Study of Hominid Evolution.Genome biology and evolution · 2026Article
- Novel antimicrobial peptides and peptide-microbiome crosstalk in Appalachian salamander skin.NPJ biofilms and microbiomes · 2025Article
- New methods on the block: Taxonomic identification of archaeological bones in resin-embedded sediments through paleoproteomics.PNAS nexus · 2025Article
- Toward a Species Search Engine: KISSE Offers a Rigorous Statistical Framework for Bone Collagen Tandem Mass Spectrometry Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
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- Enamel proteins reveal biological sex and genetic variability in southern AfricanScience (New York, N.Y.) · 2025Article
- Non-invasive molecular species identification using spider silk proteomics.Scientific reports · 2025Article
- Classification of Collagens via Peptide Ambiguation, in a Paleoproteomic LC-MS/MS-Based Taxonomic Pipeline.Journal of proteome research · 2025Article
- An unclean slate, discrepancies between food input and recovered protein signal from experimental foodcrusts.PloS one · 2025Article
- Clothomics: a practical guide to understand the opportunities and challenges of omics-based methods in archaeological cloth research.NPJ heritage science · 2025Review
- Automated High-Throughput Biological Sex Identification from Archeological Human Dental Enamel Using Targeted Proteomics.Journal of proteome research · 2024Article
- Bone Proteomics Method Optimization for Forensic Investigations.Journal of proteome research · 2024Article
- Increasing sustainability in palaeoproteomics by optimizing digestion times for large-scale archaeological bone analyses.iScience · 2024Article
- Open-tubular trap columns: towards simple and robust liquid chromatography separations for single-cell proteomics.Molecular omics · 2024Article
- The ecology, subsistence and diet of ~45,000-year-old Homo sapiens at Ilsenhöhle in Ranis, Germany.Nature ecology & evolution · 2024Article
Corrections and comments
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Authors and funding
17 authors at 7 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 for analyzing archaeological bone 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 confirm 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 produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate 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 is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.
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