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Reproducible mass s...
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Heuckeroth, SteffenUniversity of Münster, Münster, Germany
(författare)
Reproducible mass spectrometry data processing and compound annotation in MZmine 3
- Artikel/kapitelEngelska2024
Förlag, utgivningsår, omfång ...
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2024
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Nature Publishing Group,2024
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printrdacarrier
Nummerbeteckningar
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LIBRIS-ID:oai:DiVA.org:oru-113749
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https://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-113749URI
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https://doi.org/10.1038/s41596-024-00996-yDOI
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Språk:engelska
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Sammanfattning på:engelska
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Ämneskategori:ref swepub-contenttype
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Ämneskategori:for swepub-publicationtype
Anmärkningar
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Study Protocol.T.P. is supported by the Czech Science Foundation (GA CR) grant 21-11563M and by the European Union's Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement no. 891397. T.D. is supported by the European Regional Development Fund, Programme Johannes Amos Comenius project 'IOCB MSCA PF Mobility' no. CZ.02.01.01/00/22_010/0002733. C.B. is supported by the Czech Academy of Sciences Program to Support Prospective Human Resources. A.S. and X.D. are supported by the National Institutes of Health grant U01CA235507. P.C.D. is supported by R01GM107550, R03OD034493, R01DK136117 and NSF 2152526.
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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.
Ämnesord och genrebeteckningar
Biuppslag (personer, institutioner, konferenser, titlar ...)
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Damiani, TitoInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
(författare)
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Smirnov, AleksandrUniversity of North Carolina at Charlotte, Charlotte, NC, USA
(författare)
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Mokshyna, OlenaInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
(författare)
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Brungs, CorinnaInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
(författare)
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Korf, AnsgarInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
(författare)
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Smith, Joshua DavidInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic; First Faculty of Medicine, Charles University, Prague, Czech Republic
(författare)
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Stincone, PaoloUniversity of Tuebingen, Tuebingen, Germany
(författare)
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Dreolin, NicolaWaters Corporation, Wilmslow, UK
(författare)
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Nothias, Louis-FélixUniversity of Geneva, Geneva, Switzerland; Université Côte d'Azur, CNRS, ICN, Nice, France
(författare)
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Hyötyläinen, Tuulia,1971-Örebro universitet,Institutionen för naturvetenskap och teknik(Swepub:oru)tihn
(författare)
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Oresic, Matej,1967-Örebro universitet,Institutionen för medicinska vetenskaper,University of Turku and Åbo Akademi University, Turku, Finland(Swepub:oru)moc
(författare)
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Karst, UweUniversity of Münster, Münster, Germany
(författare)
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Dorrestein, Pieter C.Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
(författare)
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Petras, DanielUniversity of Tuebingen, Tuebingen, Germany; University of California Riverside, Riverside, CA, USA
(författare)
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Du, XiuxiaUniversity of North Carolina at Charlotte, Charlotte, NC, USA
(författare)
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van der Hooft, Justin J. J.Wageningen University & Research, Wageningen, the Netherlands; University of Johannesburg, Johannesburg, South Africa
(författare)
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Schmid, RobinUniversity of Münster, Münster, Germany; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
(författare)
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Pluskal, TomášInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
(författare)
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University of Münster, Münster, GermanyInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
(creator_code:org_t)
Sammanhörande titlar
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Ingår i:Nature Protocols: Nature Publishing Group1754-21891750-2799
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Heuckeroth, Stef ...
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Damiani, Tito
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Smirnov, Aleksan ...
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Mokshyna, Olena
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Brungs, Corinna
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Korf, Ansgar
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Smith, Joshua Da ...
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Stincone, Paolo
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Dreolin, Nicola
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Nothias, Louis-F ...
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Hyötyläinen, Tuu ...
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Oresic, Matej, 1 ...
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Karst, Uwe
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Dorrestein, Piet ...
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Petras, Daniel
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Du, Xiuxia
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van der Hooft, J ...
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Schmid, Robin
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Pluskal, Tomáš
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