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Integrative open workflow for confident annotation and molecular networking of metabolomics MSE/DIA data.
Katchborian-Neto, Albert; Alves, Matheus F; Bueno, Paula C P; de Jesus Nicácio, Karen; Ferreira, Miller S; Oliveira, Tiago B; Barbosa, Henrique; Murgu, Michael; de Paula Ladvocat, Ana C C; Dias, Danielle F; Soares, Marisi G; Lago, João H G; Chagas-Paula, Daniela A.
Afiliação
  • Katchborian-Neto A; Chemistry Institute, Federal University of Alfenas, 37130-001, Alfenas, Minas Gerais, Brazil.
  • Alves MF; Chemistry Institute, Federal University of Alfenas, 37130-001, Alfenas, Minas Gerais, Brazil.
  • Bueno PCP; Chemistry Institute, Federal University of Alfenas, 37130-001, Alfenas, Minas Gerais, Brazil.
  • de Jesus Nicácio K; Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany.
  • Ferreira MS; Department of Chemistry, Federal University of Mato Grosso, 14040-901, Cuiabá, Mato Grosso, Brazil.
  • Oliveira TB; Chemistry Institute, Federal University of Alfenas, 37130-001, Alfenas, Minas Gerais, Brazil.
  • Barbosa H; Department of Pharmacy, Federal University of Sergipe, 49100-000, São Cristóvão, Sergipe, Brazil.
  • Murgu M; Center of Natural Sciences and Humanities, Federal University of ABC, 09210-180, Santo Andre, São Paulo, Brazil.
  • de Paula Ladvocat ACC; Waters Corporation, Alameda Tocantins 125, Alphaville, 06455-020, São Paulo, São Paulo, Brazil.
  • Dias DF; Department of Pharmaceutical Sciences, Federal University of Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil.
  • Soares MG; Chemistry Institute, Federal University of Alfenas, 37130-001, Alfenas, Minas Gerais, Brazil.
  • Lago JHG; Chemistry Institute, Federal University of Alfenas, 37130-001, Alfenas, Minas Gerais, Brazil.
  • Chagas-Paula DA; Center of Natural Sciences and Humanities, Federal University of ABC, 09210-180, Santo Andre, São Paulo, Brazil.
Brief Bioinform ; 25(2)2024 Jan 22.
Article em En | MEDLINE | ID: mdl-38324622
ABSTRACT
Liquid chromatography coupled with high-resolution mass spectrometry data-independent acquisition (LC-HRMS/DIA), including MSE, enable comprehensive metabolomics analyses though they pose challenges for data processing with automatic annotation and molecular networking (MN) implementation. 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 'in-house' 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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Metabolômica Tipo de estudo: Prognostic_studies Idioma: En Revista: Brief Bioinform Assunto da revista: BIOLOGIA / INFORMATICA MEDICA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Brasil País de publicação: Reino Unido
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Metabolômica Tipo de estudo: Prognostic_studies Idioma: En Revista: Brief Bioinform Assunto da revista: BIOLOGIA / INFORMATICA MEDICA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Brasil País de publicação: Reino Unido