Hello,
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?
Thanks