I have an Agilent 1200 HPLC that I would like to use with our Q-Exactive HF-X mass spec, and control both the 1200 & QE with Xcalibur. This is so I can use the Agilent for some normal phase separations, while keeping our Thermo LC setup for RPLC.

The 1200 stack is a solvent tray, vacuum degasser (G1322A), quaternary pump (G1311A), autosampler (G1367B), and TCC (thermostated column compartment, GG1316A). Each module is listed as supported for use with Thermo MS, and has the compatible firmware installed.

We have Xcalibur 4.1 on the PC, with the Agilent drivers from Thermo. The Agilent 1200 connects to Xcalibur successfully, and I can use the "direct control" feature to manually control the LC pump, column compartment temperature & valve position, and autosampler. I have been able to perform a direct control injection, isocratic elution, & MS data acquisition, all through direct control in Xcalibur & the Tune window. That worked fine. I thought I was all set to begin method development in earnest, but my best laid plans, well, you know how they go some days.

The problem arises when I attempt to run a sequence in Xcalibur using an instrumental method. When I build a sequence (just a blank injection, for example) and click "run sample" or "run sequence", the LC modules and MS show "Ready to Download", the Run Manager within Xcalibur says it is "downloading" the method, and the sample is shown in the queue. But then nothing happens, and the queue goes blank. That all occurs very quickly. It is as if the 40 minute method completes in 1-2 seconds. All modules remain with "ready to download" status throughout this series of events. No errors. If I leave the system "on" after the sequence, the pump runs at whatever flow the method was set up for. If I set them to "standby" after the sequence, the pump does not run (this is the expected behavior). But the full sequence itself never runs.

Is there some sort of "wait for ready" that is missing here? I currently have the autosampler set up as the "start device". The MS never says "waiting for contact closure" and the LC injection never occurs.

I do have the BCD board installed in the LC autosampler and wired to trigger contact closure of the MS. But this doesn't come into play if the MS is never waiting for the CC signal, and the LC never performs the injection to provide the signal either.

I've followed the Thermo "Agilent 1200 Series: Getting Connected Guide for LC Devices" (from April 2014, revision H), and that leads me to think I have done everything correct. It has been no further help after getting everything talking.

I think I'm missing something simple? What I thought would be the hard part is done, but I am struggling with this one, and any insight would be greatly appreciated. Thank you in advance.