How to program custom injector program for needle wash


we wanted to minimize carry-over effect in our pesticide analysis. In order to achieve that, we wanted to program custom injector program: wash needle in vial 1 + after injection clean of the needle and seat with ACN and MeOH in vials 2 and 3. Our program looked like this: 

We use gradient program   and this method

Unfortunately, first injection was acquired partial, than second went well, but next one was acquired just "partial" and then no other sample was acquired. We use Agilent LC 1200 with MS ABSciex 4000Qtrap. Analyst program version is 1.5.1.

When we looked at the chromatograms - we didnt see any signal for partial acquired samples. We can see that LC injects - but MS dont measure. One run shoud be 22 minutes, but it didnt stopped, as you can see in the picture, we had to abort it manually. When we run a sequence without custom injector program, it runs well. 

Can somebody helps us, if the problem is in our custom injector program or can it be just the connection between LC - MS?


  • Hello  ,

    I'm not familiar with Analyst or its implementation of Agilent LC drivers, but if this program were run on an Agilent data system I would expect it to work, if the runtimes for the instrument are set appropriately. Your MS and pump runtimes are different, and I don't know how Analyst will handle that. I'm also not certain what will happen if the events in the injector program exceed the time allowed for the run. The system may go into a ready wait state while the injector program finishes. It would be best to make certain your final wash commands can all occur within the 15 to 22 minute time range before the run ends.

    I would suggest using a short isocratic program and build this injection program section by section to find out what the issue is. Start with making certain that steps 1-5 work as expected and start a run every time. Then try adding the WAIT command with no further actions and verify that data is still collected. Then add the first wash, etc. until you have a working program. 

  • Hello, thank you for your answer. We suspect the wait command to be the problem. We will try your suggestion and will see what we can do with it.

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