To showcase the jHRMS toolbox, two datasets have been used acquired on different instruments, in different labs covering both environmental and biological matrices. One dataset comprises of surface water samples measured on an Orbitrap instrument in centroided mode while the other dataset dealt with two biological matrices measured on a ZenoTOF in profile model. Brief details on the datasets are provided below as the aim of the paper is to showcase the jHRMS toolbox without going too much in depth of what is found in the data. These two different data sets have specifically been chosen to show the compatibility of the toolbox with different types of measured data and applications' purposes. Furthermore, this section contains the processing details and parameters used for showcasing the toolbox capabilities and the code availability of the jHRMS toolbox.