{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T14:30:33Z","timestamp":1787063433641,"version":"build-2736575974"},"reference-count":8,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2017,4,7]],"date-time":"2017-04-07T00:00:00Z","timestamp":1491523200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wellcome Trust","award":["107471"],"award-info":[{"award-number":["107471"]}]},{"DOI":"10.13039\/501100000836","name":"University of Liverpool","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000836","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns4:p>\n                    Experiments involving mass spectrometry (MS)-based proteomics are widely used for analyses of connective tissues. Common examples include the use of relative quantification to identify differentially expressed peptides and proteins in cartilage and tendon. We are working on characterising so-called \u2018neopeptides\u2019, i.e. peptides formed due to native cleavage of proteins, for example under pathological conditions. Unlike peptides typically quantified in MS workflows due to the\n                    <ns4:italic>in vitro<\/ns4:italic>\n                    use of an enzyme such as trypsin, a neopeptide has at least one terminus that was not due to the use of trypsin in the workflow. The identification of neopeptides within these datasets is important in understanding disease pathology, and the development of antibodies that could be utilised as diagnostic biomarkers for diseases, such as osteoarthritis, and targets for novel treatments. Our previously described neopeptide data analysis workflow was laborious and was not amenable to robust statistical analysis, which reduced confidence in the neopeptides identified. To overcome this, we developed \u2018Neopeptide Analyser\u2019, a user friendly neopeptide analysis tool used in conjunction with label-free MS quantification tool Progenesis QIP for proteomics. Neopeptide Analyser filters data sourced from Progenesis QIP output to identify neopeptide sequences, as well as give the residues that are adjacent to the peptide in its corresponding protein sequence. It also produces normalised values for the neopeptide quantification values and uses these to perform statistical tests, which are also included in the output. Neopeptide Analyser is available as a Java application for Mac, Windows and Linux. The analysis features and ease of use encourages data exploration, which could aid the discovery of novel pathways in extracellular matrix degradation, the identification of potential biomarkers and as a tool to investigate matrix turnover. Neopeptide Analyser is available from\n                    <ns4:ext-link xmlns:ns3=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" ns3:href=\"https:\/\/github.com\/PGB-LIV\/neo-pep-tool\/releases\/\">https:\/\/github.com\/PGB-LIV\/neo-pep-tool\/releases\/<\/ns4:ext-link>\n                    .\n                  <\/ns4:p>","DOI":"10.12688\/wellcomeopenres.11275.1","type":"journal-article","created":{"date-parts":[[2017,4,7]],"date-time":"2017-04-07T04:20:21Z","timestamp":1491538821000},"page":"24","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":9,"title":["Neopeptide Analyser: A software tool for neopeptide discovery in proteomics data"],"prefix":"10.12688","volume":"2","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6979-0440","authenticated-orcid":false,"given":"Mandy J.","family":"Peffers","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew R.","family":"Jones","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antony","family":"McCabe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Anderson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2017,4,7]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"106-20","DOI":"10.1002\/jor.22963","article-title":"Characterization of neopeptides in equine articular cartilage degradation.","volume":"34","author":"M Peffers","year":"2016","journal-title":"J Orthop Res."},{"key":"ref-2","doi-asserted-by":"publisher","DOI":"10.1038\/srep20455","article-title":"Anatomical heterogeneity of tendon: Fascicular and interfascicular tendon compartments have distinct proteomic composition.","volume":"6","author":"C Thorpe","year":"2016","journal-title":"Sci Rep."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"R110","DOI":"10.1186\/ar4560","article-title":"Matrix assisted laser desorption ionization mass spectrometry imaging identifies markers of ageing and osteoarthritic cartilage.","volume":"16","author":"M Peffers","year":"2014","journal-title":"Arthritis Res Ther."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"25867-78","DOI":"10.1074\/jbc.M114.566554","article-title":"Proteomic analysis reveals age-related changes in tendon matrix composition, with age- and injury-specific matrix fragmentation.","volume":"289","author":"M Peffers","year":"2014","journal-title":"J Biol Chem."},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"1204-13","DOI":"10.1016\/j.joca.2015.03.019","article-title":"Comprehensive protein profiling of synovial fluid in osteoarthritis following protein equalization.","volume":"23","author":"M Peffers","year":"2015","journal-title":"Osteoarthritis Cartilage."},{"key":"ref-6","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.4769746.v1","article-title":"Equine cartilage secretome 5 days IL-1 treatment in vitro; Progenesis semi tryptic peptides measurements file for input into the Neopeptide Analyser.","author":"M Peffers","year":"2017","journal-title":"figshare."},{"key":"ref-7","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.4772131.v1","article-title":"Equine cartilage secretome 5 days IL-1 treatment in vitro;'Neopeptide Analyser' output files.","author":"M Peffers","year":"2017","journal-title":"figshare."},{"key":"ref-8","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.438664","article-title":"PGB-LIV\/neo-pep-tool: First release, with MIT licence [Data set].","year":"2017","journal-title":"Zenodo."}],"container-title":["Wellcome Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/2-24\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/2-24\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/2-24\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,17]],"date-time":"2020-05-17T15:46:50Z","timestamp":1589730410000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/2-24\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,4,7]]},"references-count":8,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.11275.1","relation":{"has-review":[{"id-type":"doi","id":"10.21956\/wellcomeopenres.12164.r22115","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.12164.r21632","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.12164.r22115","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.12164.r21632","asserted-by":"object"}]},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,4,7]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/2-24\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.12164.r21632, Timothy E. Hardingham, Jamie Soul, Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK, 02 May 2017, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/2-24\/v1#referee-response-21632","order":0,"name":"referee-response-21632","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.12164.r22115, Stephanie G. Dakin, \u00a0Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), Nuffield Orthopaedic Centre, University of Oxford, Oxford, UK, 10 May 2017, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/2-24\/v1#referee-response-22115","order":1,"name":"referee-response-22115","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by the Wellcome Trust [107471]; and a University of Liverpool Technical Directorate Voucher. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":2,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}