Supplementary dataset for the "MAMSI: Integration of multi-assay liquid chromatography – mass spectrometry metabolomics data using multi-view machine learning" publication. This repository contains 3 dataset originating from 2 studies that were run at the UK National Phenome Centre (NPC). All of these datasets contain multi-assay metabolomics data: The AddNeuroMed study dataset was collected as part of the “European Collaboration for the Discovery of Novel Biomarkers for Alzheimer’s Disease (AD)” [1]. There are three LC-MS serum assays available: HILIC positive ionization assay (HILIC +), and lipidomic RPC positive ionization (Lipid RPC +) and negative ionization (Lipid RPC -) assays [2]. These data were converted to mzML format using ProteoWizard [3], pre-processed using XCMS [4] and nPYc toolbox [5] software resulting in 681, 4886 and 2091 features for HILIC +, lipid RPC +, and lipid RPC - respectively. A total of 577 subjects were available, 294 of those were female and 283 were male. The MY DIABETES study [6] comprises individuals of White, South Asian and African-Caribbean ancestry, mostly diagnosed with type 1 diabetes under the age of 30. Three LC-MS serum assays are available: HILIC +, Lipid RPC + and Lipid RPC -, containing 613, 1771 and 907 features respectively. There are also three urine assays: HILIC +, and RPC for small molecule separation in both positive ionization (SmMol RPC +) and negative ionization (SmMol RPC +) containing 2600, 12817 and 7142 features respectively [2]. All assays were pre-processed using ProteoWizard, XCMS and the nPYc toolbox software. A total of 984 subjects were available in this study, 540 of those were female and 444 were male. Table 1: National Phenome Centre LC-MS assay names and descriptions. NPC Assay Name CSV File Name Description HILIC + hpos HILIC positive ionisation assay Lipid RPC + lpos Lipidomic RPC positive ionisation assay Lipid RPC - lneg Lipidomic RPC negative ionisation assay SmMol RPC + rpos Small molecule separation positive ionisation assay SmMol RPC + rneg Small molecule separation negative ionisation assay