Galaxy QCxMS for Straightforward Semi-Empirical Quantum Mechanical EI-MS Prediction

High-performance computing (HPC) environments are crucial for computational research, including quantum chemistry (QC), but pose challenges for non-expert users. Researchers with limited computational knowledge struggle to utilise domain-specific software efficiently, making mass spectra prediction for in silico annotation inaccessible to many wet lab scientists. Our objective is to democratise access to semi-empirical quantum mechanical (SQM)-based predictions without requiring advanced computational skills. We provide a robust workflow that leverages interoperable file formats for molecular structures to ensure seamless integration across various QC tools. The functionality of the quantum chemistry (X) ionization mass spectrometry; X = EI or CID (QCxMS) package for electron ionisation (EI) mass spectral predictions has been integrated into the Galaxy platform to enable automated insights into EI fragmentation mechanisms. The extended tight binding (xTB) quantum chemistry package, chosen for its balance between accuracy and computational efficiency, is utilised for molecular geometry optimisation. A Docker image encapsulates the necessary software stack. We demonstrate the workflow for four molecules, highlighting the scalability and efficiency of our solution via runtime performance analysis. This work underscores how non-HPC users can perform these predictions effortlessly, using advanced computational tools without needing in-depth expertise.