The jHRMS toolbox is an open-source and open-access modular toolbox that, on one hand, provides an user interface for NTA HRMS data processing algorithms and, on the other hand, allows full freedom to modify and add workflows. The first environmental dataset that was processed with the jHRMS toolbox, showed similar trends in the data as the original study by Singh et. al. and the extensive visualization and reporting by the toolbox. Meanwhile the second workflow showcased that the algorithms are able to extract important information that can differentiate between biological tissues. Additionally, the toolbox comes with built-in statistical analysis and visualization (i.e., post-processing) at almost every point in the workflow. The specific algorithms that are implemented at the time of publication are: SAFD for the feature detection of both profile and centroided data, CompCreate for the componentization of both DDA and DIA measurements, ULSA that provides extensive reporting of match sore and quality, and suspect screening from ULSA that also screens MS2 information for fragments. Moreover, the toolbox runs on all operating systems, allows for saving parameters for specific methods, and reports algorithms results for each step in the workflow in .csv files. The latter allows for easy transfer to and from other platforms to, for example, use the feature detection results from another algorithms and proceed with the workflow in the jHRMS toolbox.