Metabolites, lipids, and other small molecules are key constituents of tissues supporting cellular programs in health and disease. Here, we present METASPACE, a community-populated knowledge base of spatial metabolomes from imaging mass spectrometry data. METASPACE is enabled by a high-performance engine for metabolite annotation in a confidence-controlled way that makes results comparable between experiments and laboratories. By sharing their results publicly, engine users continuously populate a knowledge base of annotated spatial metabolomes in tissues currently including over 3000 datasets from human cancer cohorts, whole-body sections of animal models, and various organs. The spatial metabolomes can be visualized, explored and shared using a web app as well as accessed programmatically for large-scale analysis. By using novel computational methods inspired by natural language processing, we illustrate that METASPACE provides molecular coverage beyond the capacity of any individual laboratory and opens avenues towards comprehensive metabolite atlases on the levels of tissues and organs.

Motivation:Imaging mass spectrometry (imaging MS) is a powerful technology for revealing localizations of hundreds of molecules in tissue sections. However, imaging MS data is polluted with off-sample ions caused by caused by sample preparation, particularly by the MALDI matrix application. The presence of the off-sample ion images confounds and hinders metabolite identification and downstream analysis. Results:We created a high-quality gold standard of 23238 manually tagged ion images from 87 public datasets from the METASPACE knowledge base. We developed several machine and deep learning methods for recognizing off-sample ion images. Deep residual learning performed the best with the F1 score of 0.97. Spatio-molecular biclustering method achieved the F1 scores of 0.96 and 0.93 in semi-and fully-automated scenarios, respectively. Molecular co-localization method achieved the F1 score of 0.90. We investigated the clusters of the DHB matrix, the most common MALDI matrix, and characterized parameters of a clusters combinatorial model. This 1 work addresses an important issue in imaging MS and illustrates how public data, modern web technologies, and machine and deep learning open novel avenues in imaging MS.Availability and Implementation: Data and source code are available at:https://github.com/metaspace2020/offsample .