Non-targeted chemical analysis is a powerful tool for exploration of the unknown chemistry of complex matrices such as food, biological, geochemical, environmental and even extra-terrestrial samples. It allows researchers to ask open, unbiased questions about their system chemistry. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) offers these options and has been widely used to study complex mixtures, with its unmatched mass resolution enabling direct infusion methods and eliminating the challenges of chromatographic alignment in large-scale longitudinal projects. In this article, we demonstrate the use of FT-ICR-MS for generating a dataset for hundreds of complex samples with diverse chemistries over a period of 6 years and 32 batches, allowing confident comparison of data between samples from different batches. The resulting chemical database will be continuously expanded in future and retrospectively interrogated to test new hypotheses utilizing data of past projects and new knowledge of coming projects. We discuss the experimental setup and how other researchers could apply the same approaches, which is relevant for wide ranging applications and research fields.