Workflow The developed semi-automated workflow for predicting mass spectra integrates various functions to streamline the process, significantly enhancing researchers' capacity to conduct high-throughput mass spectra simulations. To the best of our knowledge, this addresses a deficiency in available open-source end-to-end processing solutions. It includes approaches such as managing input file preparation through templates and a global parameter file for every stage of the workflow on a high-performance computing (HPC) cluster as well as accompanying scripts for batch job submission, progress monitoring, result collection and analysis.