{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T18:21:55Z","timestamp":1775586115833,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,3,16]],"date-time":"2020-03-16T00:00:00Z","timestamp":1584316800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Marie Curie International Fellowship"},{"name":"PALIMPSEST","award":["FP7-PEOPLE-2011-IEF 299101"],"award-info":[{"award-number":["FP7-PEOPLE-2011-IEF 299101"]}]},{"name":"British Academy Postdoctoral Fellowship"},{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"publisher","award":["DNRF128"],"award-info":[{"award-number":["DNRF128"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ERC Investigator","award":["295729-CodeX"],"award-info":[{"award-number":["295729-CodeX"]}]},{"name":"ERC Investigator","award":["787282"],"award-info":[{"award-number":["787282"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Classification of archaeological animal samples is commonly achieved via manual examination of matrix-assisted laser desorption\/ionization time-of-flight (MALDI-ToF) spectra. This is a time-consuming process which requires significant training and which does not produce a measure of confidence in the classification. We present a new, automated method for arriving at a classification of a MALDI-ToF sample, provided the collagen sequences for each candidate species are available. The approach derives a set of peptide masses from the sequence data for comparison with the sample data, which is carried out by cross-correlation. A novel way of combining evidence from multiple marker peptides is used to interpret the raw alignments and arrive at a classification with an associated confidence measure.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To illustrate the efficacy of the approach, we tested the new method with a previously published classification of parchment folia from a copy of the Gospel of Luke, produced around 1120\u2009C.E. by scribes at St Augustine\u2019s Abbey in Canterbury, UK. In total, 80 of the 81 samples were given identical classifications by both methods. In addition, the new method gives a quantifiable level of confidence in each classification.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software can be found at https:\/\/github.com\/bioarch-sjh\/bacollite, and can be installed in R using devtools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa181","type":"journal-article","created":{"date-parts":[[2020,3,13]],"date-time":"2020-03-13T12:36:35Z","timestamp":1584102995000},"page":"3719-3725","source":"Crossref","is-referenced-by-count":25,"title":["How to get your goat: automated identification of species from MALDI-ToF spectra"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0880-4460","authenticated-orcid":false,"given":"Simon","family":"Hickinbotham","sequence":"first","affiliation":[{"name":"BioArch , University of York, York YO10 5DD, UK"}]},{"given":"Sarah","family":"Fiddyment","sequence":"additional","affiliation":[{"name":"BioArch , University of York, York YO10 5DD, UK"},{"name":"McDonald Institute for Archaeological Research , University of Cambridge, Cambridge, CB2 3ER, UK"}]},{"given":"Timothy L","family":"Stinson","sequence":"additional","affiliation":[{"name":"North Carolina State University , Raleigh, NC 27695, USA"}]},{"given":"Matthew J","family":"Collins","sequence":"additional","affiliation":[{"name":"McDonald Institute for Archaeological Research , University of Cambridge, Cambridge, CB2 3ER, UK"},{"name":"Evogenomics Section , University of Copenhagen, Copenhagen 1307 K, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2020,3,16]]},"reference":[{"key":"2023063010282742200_btaa181-B1","doi-asserted-by":"crossref","first-page":"445","DOI":"10.3390\/ijms17040445","article-title":"Species identification of bovine, ovine and porcine type 1 collagen; comparing peptide mass fingerprinting and LC-based proteomics methods","volume":"17","author":"Buckley","year":"2016","journal-title":"Int. J. Mol. Sci"},{"key":"2023063010282742200_btaa181-B2","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1007\/978-3-319-64763-0_12","volume-title":"Zooarchaeological in Practice","author":"Buckley","year":"2018"},{"key":"2023063010282742200_btaa181-B3","doi-asserted-by":"crossref","first-page":"3843","DOI":"10.1002\/rcm.4316","article-title":"Species identification by analysis of bone collagen using matrix-assisted laser desorption\/ionisation time-of-flight mass spectrometry","volume":"23","author":"Buckley","year":"2009","journal-title":"Rapid Commun. Mass Spectrom"},{"key":"2023063010282742200_btaa181-B4","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.jas.2009.08.020","article-title":"Distinguishing between archaeological sheep and goat bones using a single collagen peptide","volume":"37","author":"Buckley","year":"2010","journal-title":"J. Archaeol. Sci"},{"key":"2023063010282742200_btaa181-B5","doi-asserted-by":"crossref","first-page":"1238","DOI":"10.3390\/nu10091238","article-title":"A MALDI-ToF MS approach for mammalian, human, and formula milks\u2019 profiling","volume":"10","author":"Di Francesco","year":"2018","journal-title":"Nutrients"},{"key":"2023063010282742200_btaa181-B6","doi-asserted-by":"crossref","first-page":"15066","DOI":"10.1073\/pnas.1512264112","article-title":"Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting","volume":"112","author":"Fiddyment","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023063010282742200_btaa181-B7","first-page":"1","article-title":"Criminal profiling through MALDI MS based technologies\u2013breaking barriers towards border-free forensic science","author":"Francese","year":"2019","journal-title":"Aust. J. Forensic Sci"},{"key":"2023063010282742200_btaa181-B8","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1126\/science.357.6349.346","article-title":"Biology of the book","volume":"357","author":"Gibbons","year":"2017","journal-title":"Science"},{"key":"2023063010282742200_btaa181-B9","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1016\/j.culher.2008.06.013","article-title":"Application of peptide mass mapping on proteins in historical mortars","volume":"10","author":"Kuckova","year":"2009","journal-title":"J. Cult. Herit"},{"key":"2023063010282742200_btaa181-B10","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1146\/annurev.biochem.77.032207.120833","article-title":"Collagen structure and stability","volume":"78","author":"Shoulders","year":"2009","journal-title":"Annu. Rev. Biochem"},{"key":"2023063010282742200_btaa181-B11","doi-asserted-by":"crossref","first-page":"4648","DOI":"10.1021\/ac100818g","article-title":"mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data","volume":"82","author":"Strohalm","year":"2010","journal-title":"Anal. Chem"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa181\/33241653\/btaa181.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/12\/3719\/50746206\/bioinformatics_36_12_3719.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/12\/3719\/50746206\/bioinformatics_36_12_3719.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T10:28:57Z","timestamp":1688120937000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/12\/3719\/5807605"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,3,16]]},"references-count":11,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2020,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa181","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,6,15]]},"published":{"date-parts":[[2020,3,16]]}}}