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Autor
Damiani, Tito 2 Korf, Ansgar 2 Pluskal, Tomáš 2 Bonciarelli, Stefano 1 Brungs, Corinna 1 Dorrestein, Pieter C 1 Dreolin, Nicola 1 Du, Xiuxia 1 Goracci, Laura 1 Heuckeroth, Steffen 1 Hyötyläinen, Tuulia 1 Karst, Uwe 1 Koehler, Nikolai 1 Krettler, Christoph A 1 Mokshyna, Olena 1 Ni, Zhixu 1 Nothias, Louis-Félix 1 Orešič, Matej 1 Pauling, Josch K 1 Petras, Daniel 1
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Pracoviště
1st Faculty of Medicine Charles Unive... 1 Bruker Daltonics GmbH and Co KG Fahre... 1 Center of Membrane Biochemistry and L... 1 Department of Chemistry Biology and B... 1 Department of Physiology Faculty of M... 1 Enveda Biosciences Boulder Colorado 8... 1 Institute of Biomedical Informatics G... 1 Institute of Organic Chemistry and Bi... 1 Institute of Organic Chemistry and Bi... 1 LipiTUM Chair of Experimental Bioinfo... 1 Skaggs School of Pharmacy and Pharmac... 1 University of California Riverside Ri... 1 University of Geneva Geneva Switzerland 1 University of Johannesburg Johannesbu... 1 University of Münster Münster Germany 1 University of North Carolina at Charl... 1 University of Tuebingen Tuebingen Ger... 1 University of Turku and Åbo Akademi U... 1 Université Côte d'Azur CNRS ICN Nice ... 1 Wageningen University and Research Wa... 1
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Autor
Damiani, Tito 2 Korf, Ansgar 2 Pluskal, Tomáš 2 Bonciarelli, Stefano 1 Brungs, Corinna 1 Dorrestein, Pieter C 1 Dreolin, Nicola 1 Du, Xiuxia 1 Goracci, Laura 1 Heuckeroth, Steffen 1 Hyötyläinen, Tuulia 1 Karst, Uwe 1 Koehler, Nikolai 1 Krettler, Christoph A 1 Mokshyna, Olena 1 Ni, Zhixu 1 Nothias, Louis-Félix 1 Orešič, Matej 1 Pauling, Josch K 1 Petras, Daniel 1
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Pracoviště
1st Faculty of Medicine Charles Unive... 1 Bruker Daltonics GmbH and Co KG Fahre... 1 Center of Membrane Biochemistry and L... 1 Department of Chemistry Biology and B... 1 Department of Physiology Faculty of M... 1 Enveda Biosciences Boulder Colorado 8... 1 Institute of Biomedical Informatics G... 1 Institute of Organic Chemistry and Bi... 1 Institute of Organic Chemistry and Bi... 1 LipiTUM Chair of Experimental Bioinfo... 1 Skaggs School of Pharmacy and Pharmac... 1 University of California Riverside Ri... 1 University of Geneva Geneva Switzerland 1 University of Johannesburg Johannesbu... 1 University of Münster Münster Germany 1 University of North Carolina at Charl... 1 University of Tuebingen Tuebingen Ger... 1 University of Turku and Åbo Akademi U... 1 Université Côte d'Azur CNRS ICN Nice ... 1 Wageningen University and Research Wa... 1
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Nejvíce citovaný článek - PubMed ID 20426402
PubMed
38769143
DOI
10.1038/s41596-024-00996-y
PII: 10.1038/s41596-024-00996-y
Knihovny.cz E-zdroje
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.
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
PubMed
36625108
PubMed Central
PMC9835057
DOI
10.1021/acs.analchem.2c04406
Knihovny.cz E-zdroje
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