by
lmh » Tue Aug 13, 2019 9:10 am
With MassLynx to be honest I'd personally recommend you never modify any part of a sample list that you've submitted to be run. By all means add new lines to the end, but editing the list in the middle can often cause terrible confusion.
In contrast to most manufacturers, the Waters sample list is what it says it is: just a list. The editor is just an editor. It might look like Agilent's sequence table or Shimadzu's batch file but it isn't. You put samples on the list, and you tell MassLynx to run rows from the list. Viewed that way, it's quite a nice concept.
For this reason, you don't need to pause the instrument when you edit the list. You can edit it at any time, adding new lines, but even if you save the list afterwards, they won't be run. They will only be run if you tell MassLynx to run them, for example by selecting them and clicking the "run" button as normal. The rows that you have submitted will now appear in the queue.
If you realise you've submitted inappropriate samples to be run, what I'd recommend is write everything the way you want it in the sample list, submit what you've written, and then delete the current item from the queue. This way, MassLynx can finish the current run and simply proceed to your new lines without confusion. The place where things get horrible is if you delete a line from the middle of a set of samples that's already been submitted; I suspect MassLynx of getting itself into a sort of frame-shift misunderstanding here where it injects samples off one line while using the name off the adjacent line, but it's probably just that I misunderstand the logic behind how it works. I asked a Waters engineer about this and his response was "just don't do it; it's too confusing!"