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This motivated the present proposal, in which we introduce DIA-IntOpenStream, a new integrated workflow combining open-source software to streamline MSE data handling. It provides \u2018in-house\u2019 custom database construction, allows the conversion of raw MSE data to a universal format (.mzML) and leverages open software (MZmine 3 and MS-DIAL) all advantages for confident annotation and effective MN data interpretation. This pipeline significantly enhances the accessibility, reliability and reproducibility of complex MSE\/DIA studies, overcoming previous limitations of proprietary software and non-universal MS data formats that restricted integrative analysis. We demonstrate the utility of DIA-IntOpenStream with two independent datasets: dataset 1 consists of new data from 60 plant extracts from the Ocotea genus; dataset 2 is a publicly available actinobacterial extract spiked with authentic standard for detailed comparative analysis with existing methods. This user-friendly pipeline enables broader adoption of cutting-edge MS tools and provides value to the scientific community. Overall, it holds promise for speeding up metabolite discoveries toward a more collaborative and open environment for research.<\/jats:p>","DOI":"10.1093\/bib\/bbae013","type":"journal-article","created":{"date-parts":[[2024,2,7]],"date-time":"2024-02-07T17:53:00Z","timestamp":1707328380000},"source":"Crossref","is-referenced-by-count":13,"title":["Integrative open workflow for confident annotation and molecular networking of metabolomics MSE\/DIA data"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2711-2881","authenticated-orcid":false,"given":"Albert","family":"Katchborian-Neto","sequence":"first","affiliation":[{"name":"Chemistry Institute, Federal University of Alfenas , 37130-001, Alfenas, Minas Gerais , Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2980-0370","authenticated-orcid":false,"given":"Matheus F","family":"Alves","sequence":"additional","affiliation":[{"name":"Chemistry Institute, Federal University of Alfenas , 37130-001, 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Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7578-9497","authenticated-orcid":false,"given":"Tiago B","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Federal University of Sergipe , 49100-000, S\u00e3o Crist\u00f3v\u00e3o, Sergipe , Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1163-9681","authenticated-orcid":false,"given":"Henrique","family":"Barbosa","sequence":"additional","affiliation":[{"name":"Center of Natural Sciences and Humanities, Federal University of ABC , 09210-180, Santo Andre, S\u00e3o Paulo , Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7489-7637","authenticated-orcid":false,"given":"Michael","family":"Murgu","sequence":"additional","affiliation":[{"name":"Waters Corporation , Alameda Tocantins 125, Alphaville, 06455-020, S\u00e3o Paulo, S\u00e3o Paulo , Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7998-0950","authenticated-orcid":false,"given":"Ana C C","family":"de Paula Ladvocat","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, Federal University of Juiz de Fora , 36036-900, Juiz de Fora, Minas Gerais , Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9129-4734","authenticated-orcid":false,"given":"Danielle F","family":"Dias","sequence":"additional","affiliation":[{"name":"Chemistry Institute, Federal University of Alfenas , 37130-001, Alfenas, Minas Gerais , Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9221-9867","authenticated-orcid":false,"given":"Marisi G","family":"Soares","sequence":"additional","affiliation":[{"name":"Chemistry Institute, Federal University of Alfenas , 37130-001, Alfenas, Minas Gerais , Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1193-8374","authenticated-orcid":false,"given":"Jo\u00e3o H G","family":"Lago","sequence":"additional","affiliation":[{"name":"Center of Natural Sciences and Humanities, Federal University of ABC , 09210-180, Santo Andre, S\u00e3o Paulo , 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