{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T12:34:52Z","timestamp":1769344492217,"version":"3.49.0"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,2,10]],"date-time":"2024-02-10T00:00:00Z","timestamp":1707523200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020","award":["FINDER-StG-715069"],"award-info":[{"award-number":["FINDER-StG-715069"]}]},{"name":"FWO Research Foundation Flanders"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Zooarchaeology by Mass Spectrometry (ZooMS) is a palaeoproteomics method for the taxonomic determination of collagen, which traditionally involves challenging manual spectra analysis with limitations in quantitative results. As the ZooMS reference database expands, a faster and reproducible identification tool is necessary. Here we present SpecieScan, an open-access algorithm for automating taxa identification from raw MALDI-ToF mass spectrometry (MS) data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>SpecieScan was developed using R (pre-processing) and Python (automation). The algorithm\u2019s output includes identified peptide markers, closest matching taxonomic group (taxon, family, order), correlation scores with the reference databases, and contaminant peaks present in the spectra. Testing on original MS data from bones discovered at Palaeothic archaeological sites, including Denisova Cave in Russia, as well as using publicly-available, externally produced data, we achieved &amp;gt;90% accuracy at the genus-level and \u223c92% accuracy at the family-level for mammalian bone collagen previously analysed manually.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The SpecieScan algorithm, along with the raw data used in testing, results, reference database, and common contaminants lists are freely available on Github (https:\/\/github.com\/mesve\/SpecieScan).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae054","type":"journal-article","created":{"date-parts":[[2024,2,10]],"date-time":"2024-02-10T03:19:32Z","timestamp":1707535172000},"source":"Crossref","is-referenced-by-count":12,"title":["SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5871-2815","authenticated-orcid":false,"given":"Emese I","family":"V\u00e9gh","sequence":"first","affiliation":[{"name":"Department of Evolutionary Anthropology, University of Vienna, University Biology Building , A-1030 Vienna, Austria"},{"name":"Human Evolution and Archaeological Sciences (HEAS), University of Vienna , Vienna, Austria"},{"name":"Archaeology, Environmental Changes, and Geochemistry, Vrije Universiteit Brussel , 1050 Brussels, Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0558-0011","authenticated-orcid":false,"given":"Katerina","family":"Douka","sequence":"additional","affiliation":[{"name":"Department of Evolutionary Anthropology, University of Vienna, University Biology Building , A-1030 Vienna, Austria"},{"name":"Human Evolution and Archaeological Sciences (HEAS), University of Vienna , Vienna, 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