The newest Thermo Scientific Compound Discoverer 3.3 software can be used by small molecule researchers to detect more compounds in less time thanks to a faster and more sensitive peak detection algorithm. Filtering large data sets down to relevant compounds is now easier by using the new peak quality functionality to streamline data processing and review. Improve confidence in compound annotations through MSn spectral tree search capabilities in tandem with the Thermo Scientific mzCloud spectral library to address the most challenging unknown compounds. Compound Discoverer 3.3 software, which has been optimised for processing large datasets and detecting low-abundance compounds, will support scientists in metabolomics, pharmaceutical, environmental, food safety, clinical and forensics applications to acquire the results they need to drive science forward.