Regardless, manual assignment and validation of molecular isotopic envelopes can take up to several hours or more per analysis and require the use of multiple tools depending on the specific restrictions per tool and the aims of the analysis. Centralizing the steps of the bioinformatics workflow, which includes sequence to molecular formula conversion, the addition of known and unknown mass shifts, and isotopic matching, within IsoMatchMS allows for a preliminary analysis of highresolution MALDI-MS with an experimental or protein sequence database within minutes. This improvement in speed allows for more high-throughput analyses of MALDI-MS data and reduces the knowledge burden associated with using several tools to process data for different types of molecules. While the curation of an experimental or protein sequence database still requires sample dependent supplemental efforts, this tool vastly improves the throughput and reproducibility of MALDI-MS workflows for biomolecules. As more experimental data become available in public repositories, scoring matches may be improved to the point of fully automated peak annotations.