Update workflow to incorporate MALDIquantForeign and MALDIquant

[LizzyParkerPannell]

Now that we've sorted the file conversion parameters to get MALDIquant to work in R, can adapt the workflow with MassUp being optional (still good for QC)

• update R codes for step 04_data-preprocessing (MALDI and DIMS)
• update guide/ documentation to explain the options
• link directly to MALDIquantForeign and MALDIquant vignettes as these are very good

[LizzyParkerPannell]

@Jkellaway is this what you were talking about yesterday? I've got it working on somebody else's data now so hoping to share notes soon