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Hoffmann N, Mayer G, Has C, Kopczynski D, Al Machot F, Schwudke D, Ahrends R, Marcus K, Eisenacher M, Turewicz M. A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. Metabolites 2022; 12:metabo12070584. [PMID: 35888710 PMCID: PMC9319858 DOI: 10.3390/metabo12070584] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 12/13/2022] Open
Abstract
Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography−mass spectrometry, ion mobility or MS imaging approaches on MS1 and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer.
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Affiliation(s)
- Nils Hoffmann
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences (IBG-5), 52425 Jülich, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
| | - Gerhard Mayer
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany;
| | - Canan Has
- Biological Mass Spectrometry, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany;
- University Hospital Carl Gustav Carus, 01307 Dresden, Germany
- CENTOGENE GmbH, 18055 Rostock, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Fadi Al Machot
- Faculty of Science and Technology, Norwegian University for Life Science (NMBU), 1433 Ås, Norway;
| | - Dominik Schwudke
- Bioanalytical Chemistry, Forschungszentrum Borstel, Leibniz Lung Center, 23845 Borstel, Germany;
- Airway Research Center North, German Center for Lung Research (DZL), 23845 Borstel, Germany
- German Center for Infection Research (DZIF), TTU Tuberculosis, 23845 Borstel, Germany
| | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Katrin Marcus
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
| | - Martin Eisenacher
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Michael Turewicz
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Düsseldorf, 85764 Neuherberg, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
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Johnson D, Batista D, Cochrane K, Davey RP, Etuk A, Gonzalez-Beltran A, Haug K, Izzo M, Larralde M, Lawson TN, Minotto A, Moreno P, Nainala VC, O'Donovan C, Pireddu L, Roger P, Shaw F, Steinbeck C, Weber RJM, Sansone SA, Rocca-Serra P. ISA API: An open platform for interoperable life science experimental metadata. Gigascience 2021; 10:giab060. [PMID: 34528664 PMCID: PMC8444265 DOI: 10.1093/gigascience/giab060] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/19/2021] [Accepted: 08/23/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The Investigation/Study/Assay (ISA) Metadata Framework is an established and widely used set of open source community specifications and software tools for enabling discovery, exchange, and publication of metadata from experiments in the life sciences. The original ISA software suite provided a set of user-facing Java tools for creating and manipulating the information structured in ISA-Tab-a now widely used tabular format. To make the ISA framework more accessible to machines and enable programmatic manipulation of experiment metadata, the JSON serialization ISA-JSON was developed. RESULTS In this work, we present the ISA API, a Python library for the creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats by using a common data model engineered as Python object classes. We describe the ISA API feature set, early adopters, and its growing user community. CONCLUSIONS The ISA API provides users with rich programmatic metadata-handling functionality to support automation, a common interface, and an interoperable medium between the 2 ISA formats, as well as with other life science data formats required for depositing data in public databases.
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Affiliation(s)
- David Johnson
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
- Department of Informatics and Media, Uppsala University, Box 513, 75120 Uppsala, Sweden
| | - Dominique Batista
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Keeva Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Robert P Davey
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Anthony Etuk
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Alejandra Gonzalez-Beltran
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
- Science and Technology Facilities Council, Scientific Computing Department, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Genome Research Limited, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden, CB10 1RQ, UK
| | - Massimiliano Izzo
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Martin Larralde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Thomas N Lawson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Alice Minotto
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Venkata Chandrasekhar Nainala
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Luca Pireddu
- Distributed Computing Group, CRS4: Center for Advanced Studies, Research & Development in Sardinia, Pula 09050, Italy
| | - Pierrick Roger
- CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France
| | - Felix Shaw
- Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Christoph Steinbeck
- Cheminformatics and Computational Metabolomics, Institute for Analytical Chemistry, Lessingstr. 8, 07743 Jena, Germany
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
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