Lipid metabolism is recognised as being central to growth, disease and health. Lipids, therefore, have an important place in current research on globally significant topics such as food security and biodiversity loss. However, answering questions in these important fields of research requires not only identification and measurement of lipids in a wider variety of sample types than ever before, but also hypothesis-driven analysis of the resulting 'big data'. We present a novel pipeline that can collect data from a wide range of biological sample types, taking 1 000 000 lipid measurements per 384 well plate, and analyse the data systemically. We provide evidence of the power of the tool through proof-of-principle studies using edible fish (mackerel, bream, seabass) and colonies of Bombus terrestris. Bee colonies were found to be more like mini-ecosystems and there was evidence for considerable changes in lipid metabolism in bees through key developmental stages. This is the first report of either high throughput LCMS lipidomics or systemic analysis in individuals, colonies and ecosystems. This novel approach provides new opportunities to analyse metabolic systems at different scales at a level of detail not previously feasible, to answer research questions about societally important topics.

Bioinformatics Core Wellcome MRC Institute of Metabolic Science University of Cambridge Addenbrooke's Treatment Centre Keith Day Road Cambridge CB2 0QQ UK

Core Metabolomics and Lipidomics Laboratory Wellcome MRC Institute of Metabolic Science University of Cambridge Addenbrooke's Treatment Centre Keith Day Road Cambridge CB2 0QQ UK

Department of Biological Sciences Royal Holloway College University of London Egham Surrey TW20 0EX UK

Department of Zoology The David Attenborough Centre University of Cambridge Corn Exchange St Cambridge CB2 3QZ UK

Department of Zoology University of Oxford Oxford OX1 3SZ UK

Institute of Botany Czech Academy of Sciences Department of Phycology Dukelská 135 379 01 Třeboň Czech Republic

Lifespan and Population Health School of Medicine University of Nottingham Nottingham NG7 2UH UK

Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1a 04103 Leipzig Sachsen Germany

Natural Resources Institute University of Greenwich Chatham Kent ME4 4TB UK

Royal Botanic Gardens Kew Kew Green Richmond Surrey TW9 3AE UK

School of Biological Sciences Faculty of Environmental and Life Sciences University of Southampton University Road Southampton SO17 1BJ UK

SpectralWorks Limited The Heath Business and Technical Park Runcorn Cheshire WA7 4EB UK

Wellcome MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit University of Cambridge Keith Day Road Cambridge CB2 0QQ UK

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