The Polyomics integrated Metabolomics Pipeline (PiMP) fulfils an unmet need in metabolomics data analysis. PiMP offers automated and user-friendly analysis from mass spectrometry data acquisition to biological interpretation. Our key innovations are the Summary Page, which provides a simple overview of the experiment in the format of a scientific paper, containing the key findings of the experiment along with associated metadata, and the Metabolite Page, which provides a list of each metabolite accompanied by evidence cards, which provide a variety of criteria behind metabolite annotation including peak shapes, intensities in different sample groups and database information.