Chromatography Forum

I'm trying to set up a sequence table in Chemstation (Rev B.03.02, Agilent 1200) that automates initial column equilibration, my prep runs, then a final column wash. The initial column equilibration consists of a gradient from 100% acetonitrile to 100% 30 mM NH4OAc (aq). I have therefore set 100% acetonitrile in the "Solvent" section of the "Set up pump" dialogue box to avoid shocking the column, which is stored in acetonitrile. At the end of the equilibration, the column is indeed in 100% 30 mM NH4OAc as intended; however, when the Stop Time is reached, the mobile phase conditions revert to the initial 100% acetonitrile for a minute or so, while data processing and injection of my prep sample occurs.

Is there a way to prevent this reversion from occurring, so that there is a seamless mobile phase transition (staying at 100% 30 mM NH4OAc) between the end of my equilibration run and the start of my prep run? Thanks.

I think what's happening is that Chemstation reverts to the flow conditions/solvent mix in the "isocratic" section of the pump control at any time before the gradient starts, and after the gradient is finished.

I'm not sure there's a way to stop it doing this, but what you could try is putting the flow to zero in the flow box at the top right, and specifying the actual flow you want, only in the gradient table. I haven't tried this, but I think that would mean that chemstation would pump 100% acetonitrile (or whatever you specify) at zero flow until it's ready to start the gradient. It would then run the gradient, and when it's finished, revert to zero flow, so although technically the solvent mix is wrong, none of it is reaching the column. The down-side would be a pressure disturbance before your first real run. In my case I always run a blank that I throw away as my first sample. It wastes instrument time, but it means all subsequent injections start with the column in the same defined state.

top left even

Make three separate Methods.M. Run as a Sequence, like with Method1.M as first line, Method2.M as second line, etc. If you like you can program in a set wait time for every time a new Method.M is loaded.

And make use of your post run time command for your Methods as well, to re-equilibrate after gradient runs.

lmh, that seems to be working nicely! Thanks for the advice!