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Lipids are of particular interest, as they influence important biological processes in health and disease. However, the identification of lipids in MALDI-MSI remains a challenge due to the lack of chromatographic separation or untargeted tandem mass spectrometry. Recent studies have proposed the use of MALDI in-source fragmentation to infer structural information and aid identification. Here we present rMSIfragment, an open-source R package that exploits known adducts and fragmentation pathways to confidently annotate lipids in MALDI-MSI. The annotations are ranked using a novel score that demonstrates an area under the curve of 0.7 in ROC analyses using HPLC\u2013MS and Target-Decoy validations. rMSIfragment applies to multiple MALDI-MSI sample types and experimental setups. Finally, we demonstrate that overlooking in-source fragments increases the number of incorrect annotations. Annotation workflows should consider in-source fragmentation\u00a0tools such as rMSIfragment to increase annotation confidence and reduce the number of false positives.<\/jats:p>","DOI":"10.1186\/s13321-023-00756-2","type":"journal-article","created":{"date-parts":[[2023,9,15]],"date-time":"2023-09-15T08:01:54Z","timestamp":1694764914000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation"],"prefix":"10.1186","volume":"15","author":[{"given":"Gerard","family":"Baquer","sequence":"first","affiliation":[]},{"given":"Lluc","family":"Sement\u00e9","sequence":"additional","affiliation":[]},{"given":"Pere","family":"R\u00e0fols","sequence":"additional","affiliation":[]},{"given":"Luc\u00eda","family":"Mart\u00edn-Saiz","sequence":"additional","affiliation":[]},{"given":"Christoph","family":"Bookmeyer","sequence":"additional","affiliation":[]},{"given":"Jos\u00e9 A.","family":"Fern\u00e1ndez","sequence":"additional","affiliation":[]},{"given":"Xavier","family":"Correig","sequence":"additional","affiliation":[]},{"given":"Mar\u00eda","family":"Garc\u00eda-Altares","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,9,15]]},"reference":[{"key":"756_CR1","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1007\/978-1-4939-6747-6_23","volume":"1550","author":"R Adusumilli","year":"2017","unstructured":"Adusumilli R, Mallick P (2017) Data conversion with ProteoWizard msConvert. 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