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Reproducible mass spectrometry data processing and compound annotation in MZmine 3.
Heuckeroth, Steffen; Damiani, Tito; Smirnov, Aleksandr; Mokshyna, Olena; Brungs, Corinna; Korf, Ansgar; Smith, Joshua David; Stincone, Paolo; Dreolin, Nicola; Nothias, Louis-Félix; Hyötyläinen, Tuulia; Oresic, Matej; Karst, Uwe; Dorrestein, Pieter C; Petras, Daniel; Du, Xiuxia; van der Hooft, Justin J J; Schmid, Robin; Pluskal, Tomás.
Afiliación
  • Heuckeroth S; University of Münster, Münster, Germany.
  • Damiani T; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
  • Smirnov A; University of North Carolina at Charlotte, Charlotte, NC, USA.
  • Mokshyna O; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
  • Brungs C; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
  • Korf A; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
  • Smith JD; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
  • Stincone P; First Faculty of Medicine, Charles University, Prague, Czech Republic.
  • Dreolin N; University of Tuebingen, Tuebingen, Germany.
  • Nothias LF; Waters Corporation, Wilmslow, UK.
  • Hyötyläinen T; University of Geneva, Geneva, Switzerland.
  • Oresic M; Université Côte d'Azur, CNRS, ICN, Nice, France.
  • Karst U; Örebro University, Örebro, Sweden.
  • Dorrestein PC; Örebro University, Örebro, Sweden.
  • Petras D; University of Turku and Åbo Akademi University, Turku, Finland.
  • Du X; University of Münster, Münster, Germany.
  • van der Hooft JJJ; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
  • Schmid R; University of Tuebingen, Tuebingen, Germany.
  • Pluskal T; University of California Riverside, Riverside, CA, USA.
Nat Protoc ; 19(9): 2597-2641, 2024 Sep.
Article en En | MEDLINE | ID: mdl-38769143
ABSTRACT
Untargeted mass spectrometry (MS) experiments produce complex, multidimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and convert it into a more comprehensible format. Depending on the sample type and/or goal of the study, a variety of MS platforms can be used for such analysis. MZmine is an open-source software for the processing of raw spectral data generated by different MS platforms. Examples include liquid chromatography-MS, gas chromatography-MS and MS-imaging. These data might typically be associated with various applications including metabolomics and lipidomics. Moreover, the third version of the software, described herein, supports the processing of ion mobility spectrometry (IMS) data. The present protocol provides three distinct procedures to perform feature detection and annotation of untargeted MS data produced by different instrumental setups liquid chromatography-(IMS-)MS, gas chromatography-MS and (IMS-)MS imaging. For training purposes, example datasets are provided together with configuration batch files (i.e., list of processing steps and parameters) to allow new users to easily replicate the described workflows. Depending on the number of data files and available computing resources, we anticipate this to take between 2 and 24 h for new MZmine users and nonexperts. Within each procedure, we provide a detailed description for all processing parameters together with instructions/recommendations for their optimization. The main generated outputs are represented by aligned feature tables and fragmentation spectra lists that can be used by other third-party tools for further downstream analysis.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Espectrometría de Masas / Programas Informáticos Idioma: En Revista: Nat Protoc Año: 2024 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Espectrometría de Masas / Programas Informáticos Idioma: En Revista: Nat Protoc Año: 2024 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Reino Unido