{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T09:11:12Z","timestamp":1784365872195,"version":"3.55.0"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,7,29]],"date-time":"2024-07-29T00:00:00Z","timestamp":1722211200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,7,29]],"date-time":"2024-07-29T00:00:00Z","timestamp":1722211200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Research Infrastructure RECETOX RI","award":["LM2023069"],"award-info":[{"award-number":["LM2023069"]}]},{"name":"European Union\u2019s Horizon 2020 research and innovation programme","award":["857560"],"award-info":[{"award-number":["857560"]}]},{"name":"Open Access funding enabled and organized by Projekt DEAL"},{"name":"Hochschule D\u00fcsseldorf University of Applied Sciences"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Mass spectral libraries have proven to be essential for mass spectrum annotation, both for library matching and training new machine learning algorithms. A key step in training machine learning models is the availability of high-quality training data. Public libraries of mass spectrometry data that are open to user submission often suffer from limited metadata curation and harmonization. The resulting variability in data quality makes training of machine learning models challenging. Here we present a library cleaning pipeline designed for cleaning tandem mass spectrometry library data. The pipeline is designed with ease of use, flexibility, and reproducibility as leading principles.<\/jats:p>\n                  <jats:p>\n                    <jats:bold>Scientific contribution<\/jats:bold>\n                  <\/jats:p>\n                  <jats:p>This pipeline will result in cleaner public mass spectral libraries that will improve library searching and the quality of machine-learning training datasets in mass spectrometry. This pipeline builds on previous work by adding new functionality for curating and correcting annotated libraries, by validating structure annotations. Due to the high quality of our software, the reproducibility, and improved logging, we think our new pipeline has the potential to become the standard in the field for cleaning tandem mass spectrometry libraries.<\/jats:p>\n                  <jats:p>\n                    <jats:bold>Graphical Abstract<\/jats:bold>\n                  <\/jats:p>","DOI":"10.1186\/s13321-024-00878-1","type":"journal-article","created":{"date-parts":[[2024,7,29]],"date-time":"2024-07-29T06:03:44Z","timestamp":1722233024000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Reproducible MS\/MS library cleaning pipeline in matchms"],"prefix":"10.1186","volume":"16","author":[{"given":"Niek F.","family":"de Jonge","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helge","family":"Hecht","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Strobel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingxun","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin J. J.","family":"van der Hooft","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Huber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,7,29]]},"reference":[{"issue":"6","key":"878_CR1","doi-asserted-by":"publisher","first-page":"1954","DOI":"10.1038\/s41596-020-0317-5","volume":"15","author":"AT Aron","year":"2020","unstructured":"Aron AT, Gentry EC, McPhail KL, Nothias L-F, Nothias-Esposito M, Bouslimani A, Petras D, Gauglitz JM, Sikora N, Vargas F (2020) Reproducible molecular networking of untargeted mass spectrometry data using GNPS. 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All other authors declare no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"88"}}