Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

Babraham Institute Babraham Research Campus Cambridge UK

Biological Science Division Pacific Northwest National Laboratory Richland WA USA

Bruker Daltonics GmbH and Co KG Bremen Germany

Center for Biotechnology University of Bielefeld Bielefeld Germany

Center of Membrane Biochemistry and Lipid Research Faculty of Medicine Carl Gustav Carus of TU Dresden Dresden Germany

Department of Analytical Chemistry University of Vienna Vienna Austria

Department of Bioengineering University of California San Diego CA USA

Department of Bioinformatics BiGCaT NUTRIM Maastricht University Maastricht The Netherlands

Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Tokyo Japan

Department of Chemistry Biology and Biotechnology University of Perugia Perugia Italy

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton UK

Field of Excellence BioHealthe University of Graz Graz Austria

Graduate School of Medical Life Science Yokohama City University Yokohama Japan

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic

Institute of Parasitology McGill University Montreal Canada

Institute of Pharmaceutical Sciences University of Graz Graz Austria

Maastricht Centre for Systems Biology Maastricht University Maastricht The Netherlands

Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany

RIKEN Center for Integrative Medical Sciences Yokohama Japan

RIKEN Center for Sustainable Resource Science Yokohama Japan

Scripps Center for Metabolomics and Mass Spectrometry The Scripps Research Institute La Jolla CA USA

Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany

Swiss Prot group SIB Swiss Institute of Bioinformatics Centre Medical Universitaire Geneva Switzerland

Systems Immunity Research Institute School of Medicine Cardiff University Cardiff UK

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