{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T00:23:01Z","timestamp":1772151781707,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,13]],"date-time":"2020-01-13T00:00:00Z","timestamp":1578873600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Nestle Research"},{"DOI":"10.13039\/501100014373","name":"Institut de Bioenginyeria de Catalunya","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100014373","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014373","name":"IBEC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100014373","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Nuclear magnetic resonance (NMR)-based metabolomics is widely used to obtain metabolic fingerprints of biological systems. While targeted workflows require previous knowledge of metabolites, prior to statistical analysis, untargeted approaches remain a challenge. Computational tools dealing with fully untargeted NMR-based metabolomics are still scarce or not user-friendly. Therefore, we developed AlpsNMR (Automated spectraL Processing System for NMR), an R package that provides automated and efficient signal processing for untargeted NMR metabolomics. AlpsNMR includes spectra loading, metadata handling, automated outlier detection, spectra alignment and peak-picking, integration and normalization. The resulting output can be used for further statistical analysis. AlpsNMR proved effective in detecting metabolite changes in a test case. The tool allows less experienced users to easily implement this workflow from spectra to a ready-to-use dataset in their routines.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The AlpsNMR R package and tutorial is freely available to download from http:\/\/github.com\/sipss\/AlpsNMR under the MIT license.<\/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\/btaa022","type":"journal-article","created":{"date-parts":[[2020,1,10]],"date-time":"2020-01-10T20:10:42Z","timestamp":1578687042000},"page":"2943-2945","source":"Crossref","is-referenced-by-count":28,"title":["AlpsNMR: an R package for signal processing of fully untargeted NMR-based metabolomics"],"prefix":"10.1093","volume":"36","author":[{"given":"Francisco","family":"Madrid-Gambin","sequence":"first","affiliation":[{"name":"Signal and Information Processing for Sensing Systems , Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8994-1549","authenticated-orcid":false,"given":"Sergio","family":"Oller-Moreno","sequence":"additional","affiliation":[{"name":"Signal and Information Processing for Sensing Systems , Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9790-6287","authenticated-orcid":false,"given":"Luis","family":"Fernandez","sequence":"additional","affiliation":[{"name":"Signal and Information Processing for Sensing Systems , Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain"},{"name":"Department of Electronics and Biomedical Engineering , Universitat de Barcelona, Barcelona 08028, Spain"}]},{"given":"Simona","family":"Bartova","sequence":"additional","affiliation":[{"name":"Nestl\u00e9 Research , EPFL Innovation Park, 1015 Lausanne, Switzerland"}]},{"given":"Maria Pilar","family":"Giner","sequence":"additional","affiliation":[{"name":"Nestl\u00e9 Research , EPFL Innovation Park, 1015 Lausanne, Switzerland"}]},{"given":"Christopher","family":"Joyce","sequence":"additional","affiliation":[{"name":"Nestl\u00e9 Research , EPFL Innovation Park, 1015 Lausanne, Switzerland"}]},{"given":"Francesco","family":"Ferraro","sequence":"additional","affiliation":[{"name":"Nestl\u00e9 Research , EPFL Innovation Park, 1015 Lausanne, Switzerland"}]},{"given":"Ivan","family":"Montoliu","sequence":"additional","affiliation":[{"name":"Nestl\u00e9 Research , EPFL Innovation Park, 1015 Lausanne, Switzerland"}]},{"given":"Sofia","family":"Moco","sequence":"additional","affiliation":[{"name":"Nestl\u00e9 Research , EPFL Innovation Park, 1015 Lausanne, Switzerland"}]},{"given":"Santiago","family":"Marco","sequence":"additional","affiliation":[{"name":"Signal and Information Processing for Sensing Systems , Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain"},{"name":"Department of Electronics and Biomedical Engineering , Universitat de Barcelona, Barcelona 08028, Spain"}]}],"member":"286","published-online":{"date-parts":[[2020,1,13]]},"reference":[{"key":"2023013111475586700_btaa022-B1","doi-asserted-by":"crossref","first-page":"23","DOI":"10.3389\/fbioe.2015.00023","article-title":"Analytical methods in untargeted metabolomics: state of the art in 2015","volume":"3","author":"Alonso","year":"2015","journal-title":"Front. 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