One of the main advantages of the jHRMS toolbox is the combination of the modular implementation of the workflow steps and full access to all the implemented algorithms. The latter will be further discussed after the advantages of the implemented algorithms. Figure shows the currently implemented algorithms in the modular workflow. It should be noted that various types of data can be analyzed, including MS1, DDA, PRM, DIA, SWATH, and multi-collision analysis. These data types can also be combined during the alignment.