Year: 2024
Type: preprint
Abstract: Untargeted MS experiments produce complex, multi-dimensional 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. Based on the sample type and/or goal of the study, a variety of MS platforms can be used for such analysis. MZmine is open-source software for the processing of raw spectral data generated by different MS platforms: liquid chromatography–MS (LC–MS), gas chromatography–MS (GC–MS), and MS–imaging. 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: LC–(IMS–)MS, GC–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 hours for new MZmine users and non-experts. 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.
Source: ChemRxiv
Authors: Tito Damiani, Steffen Heuckeroth, Aleksandr Smirnov, Olena Mokshyna, Corinna Brungs, Ansgar Korf, Joshua Smith, Paolo Stincone, Nicola Dreolin, Louis-Félix Nothias, Tuulia Hyötyläinen, Matej Orešič, Uwe Karst, Pieter Dorrestein, Daniel Petras, Xiuxia Du, Justin van der Hooft, Robin Schmid, Tomáš Pluskal
Institutions: Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry, University of Münster, University of North Carolina at Charlotte, Czech Academy of Sciences, Bruker (Germany), University of California, Santa Barbara, Charles University, University of Tübingen, Waters (United Kingdom), University of Geneva, Centre National de la Recherche Scientifique, Université Côte d'Azur, Örebro University, University of Turku, Turku Centre for Biotechnology, University of California San Diego, University of California San Diego Medical Center, University of California, Riverside, University of Johannesburg, Wageningen University & Research
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: Cross Repository Metabolomics Data and Workflow Integration, G2678520069, G291036901, G3735356012, G434337789, Linking Mass Spectrometry Computational Ecosystems to Enhance Biological Insights of Publicly-Available Data, Identification of molecular targets of psychoactive kavalactones using iBodies, Mapping the chemodiversity of Piperaceae plants using next-generation MZmine platform, G8281011517, G9000150993, G9000241751
OpenAlex ID: W4392656629