After code-refactoring, the following features are no longer supported in the simulated mass spec. They should be re-implemented at some point:
Being able to define multiple isolation windows for one MS2 scan, see here. Also some unit tests for this have been commented out, make sure to uncomment them.
Functional chromatograms only support Gaussian shapes, not gamma or uniform as before, see here.
After code-refactoring, the following features are no longer supported in the simulated mass spec. They should be re-implemented at some point: