In addition to executing a single method of fragmentation, MORTAR offers the option of executing fragmentation pipelines, which can be defined and executed with any combination of the integrated fragmentation algorithms where each selected algorithm may have its own individual settings. The Pipeline Settings view (see Figure ) provides a straightforward way to create a pipeline by adding new methods via buttons and choice boxes. A simple application example of the pipelining functionality is to apply a Sugar Removal Utility (SRU) processing step to remove terminal glycosidic moieties from the studied molecules, as it is usually done in chemical space analyses prior to another fragmentation step to avoid redundancies. Fragmentation can be started via the Fragment button.