{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T04:27:48Z","timestamp":1775190468287,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:00:00Z","timestamp":1740182400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Computational Life Sciences"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Proteome studies frequently encounter challenges in down-stream data analysis due to limited bioinformatics resources, rapid data generation, and variations in analytical methods. To address these issues, we developed SpectroPipeR, an R package designed to streamline data analysis tasks and provide a comprehensive, standardized pipeline for Spectronaut\u00ae DIA-MS data. This novel package automates various analytical processes, including XIC plots, ID rate summary, normalization, batch and covariate adjustment, relative protein quantification, multivariate analysis, and statistical analysis, while generating interactive HTML reports for e.g. ELN systems.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The SpectroPipeR package (manual: https:\/\/stemicha.github.io\/SpectroPipeR\/) was written in R and is freely available on GitHub (https:\/\/github.com\/stemicha\/SpectroPipeR).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf086","type":"journal-article","created":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T14:16:57Z","timestamp":1740233817000},"source":"Crossref","is-referenced-by-count":15,"title":["SpectroPipeR\u2014a streamlining post Spectronaut\u00ae DIA-MS data analysis R package"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6550-0132","authenticated-orcid":false,"given":"Stephan","family":"Michalik","sequence":"first","affiliation":[{"name":"Department Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, MV 17475,","place":["Germany"]}]},{"given":"Elke","family":"Hammer","sequence":"additional","affiliation":[{"name":"Department Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, MV 17475,","place":["Germany"]},{"name":"German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald , Greifswald 17475,","place":["Germany"]}]},{"given":"Leif","family":"Steil","sequence":"additional","affiliation":[{"name":"Department Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, MV 17475,","place":["Germany"]}]},{"given":"Manuela Gesell","family":"Salazar","sequence":"additional","affiliation":[{"name":"Department Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, MV 17475,","place":["Germany"]}]},{"given":"Christian","family":"Hentschker","sequence":"additional","affiliation":[{"name":"Department Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, MV 17475,","place":["Germany"]}]},{"given":"Kristin","family":"Surmann","sequence":"additional","affiliation":[{"name":"Department Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, MV 17475,","place":["Germany"]}]},{"given":"Larissa M","family":"Busch","sequence":"additional","affiliation":[{"name":"Department Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, MV 17475,","place":["Germany"]}]},{"given":"Thomas","family":"Sura","sequence":"additional","affiliation":[{"name":"Department Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, MV 17475,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5689-3448","authenticated-orcid":false,"given":"Uwe","family":"V\u00f6lker","sequence":"additional","affiliation":[{"name":"Department Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, MV 17475,","place":["Germany"]},{"name":"German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald , Greifswald 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