I'm hoping to disable the gap filling setting in alignment while using the msd console app? I don't see this parameter listed in the example files.
More generally, is there a comprehensive list of parameters that can be controlled for LCMSDDA than what appears in the example methods.txt file? This would be very helpful!
I am trying to automate a workflow using compMS where I need to convert my input files to .ABF before running compms for LCMSDDA. We noticed some missing peaks when using MZML files as inputs. Is there any way to use ABF convert as part of a batch script? I have not been able to make the .exe files in the ABF convert download work on the command line.