We present Mass Spectrometry-Data Independent Analysis software version 4 (MS-DIAL 4), a comprehensive lipidome atlas with retention time, collision cross-section and tandem mass spectrometry information. We formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry. Using human, murine, algal and plant biological samples, we annotated and semiquantified 8,051 lipids using MS-DIAL 4 with a 1-2% estimated false discovery rate. MS-DIAL 4 helps standardize lipidomics data and discover lipid pathways.

Bruker Yokohama Japan

Department of Applied Genomics Kazusa DNA Research Institute Chiba Japan

Department of Environmental Health Sciences Yale School of Public Health New Haven CT USA

Department of Genetics The Graduate University for Advanced Studies SOKENDAI Miura Japan

Department of Pathology University of Florida Gainsville FL USA

Graduate School of Bioresources Mie University Tsu Japan

Graduate School of Information Science and Technology Osaka University Osaka Japan

Graduate School of Medical Life Science Yokohama City University Yokohama Japan

Graduate School of Pharmaceutical Sciences Chiba University Chiba Japan

Graduate School of Pharmaceutical Sciences Keio University Tokyo Japan

Institute of Physiology of the Czech Academy of Sciences Prague Czech Republic

Interdisciplinary Research Center on Biology and Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai China

National Institute of Genetics Mishima Japan

NGAlab Tarragona Spain

RIKEN Center for Integrative Medical Sciences Yokohama Japan

RIKEN Center for Sustainable Resource Science Yokohama Japan

University of Chinese Academy of Sciences Beijing China

West Coast Metabolomics Center UC Davis Davis CA USA

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