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Stanford-ChEMH-MCAC / protocols

Laboratory protocols used by the Metabolite Chemistry Analysis Center, a ChEM-H Knowledge Center at Stanford University.
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6470 QQQ cannot suck calibrant into the ion source #25

Closed curt-f closed 5 years ago

curt-f commented 5 years ago

First reported by @awawro: the 6470 cannot suck calibrant from the bottle on the front of the instrument to the ion source. Instead of calibrant solution flowing up the inlet tube, little gas bubbles of nitrogen often flow down the inlet, into the bottle.

Without calibrant reaching the instrument, all Check Tune and Autotune attempts fail because there is no calibrant signal.

curt-f commented 5 years ago

@awawro and I troubleshot this issue together for ~ 1 hour last Thursday.

  1. The bottle headspace was and remained pressurized with nitrogen, so that is not the problem.

  2. None of the lines from the bottle to the LC-MS seemed clogged. The beige capillary from the calibrant delivery system valve to the 6-way switching valve for LC vs. waste vs. calibrant seemed difficult to force water through manually w/ a syringe, but not completely clogged.

  3. I called Agilent today. They informed me there is a tiny frit in the aforementioned beige capillary, and that it often becomes clogges with polymerized acetonitrile. The recommended hooking up this capillary to the LC-MS and flowing large volumes of water through it, which often resolves the problem.

curt-f commented 5 years ago

I will try to do Agilent's recommendation when the current run is over.

curt-f commented 5 years ago

We connected the capillary in question to the LC and pumped large volumes of pH 9 water and later of pH 9 acetonitrile through the capillary at 5 mL / min; no clogs were evident. When we reconnected the capillary to the "CDS" (Agilent-ese for Calibrant Delivery System), we observed a fast stream of gas bubbles coming out of the calibrant inlet tube. Eventually these dissipated and a very slow stream of calibrant made its way up the inlet tube. We waited to see if the MS could ever see any calibrant ions, but did not see any even after ~10 min of waiting.

curt-f commented 5 years ago

Email to Agilent asking for on-site service sent.

curt-f commented 5 years ago

Agilent Service Order #6003187726

curt-f commented 5 years ago

An Agilent FSE came to replace the entire CDS today. But to both our suprises, the old CDS suddenly seemed to be working fine. The instrument passed Check Tune with flying colors.

((One small new trick I learned: one (322) of the calibrant ions had lower intensities than the other. He went to “Manual Tune” and clicked the “MS1" tab, and clicked the “Adjust Gain & Offset” button. This sharply boosted the 322 peak intensity in 2-3 minutes. I think it performs a very small subset of parameters compared to a full “Autotune”, only on Q1.))

I will leave this issue open for now, but hope to close it in a week or two if there are no further reports of any problems. No idea how this seems to have automagically fixed itself.

curt-f commented 5 years ago

Closing this in lack of any further notice of failure. Will reopen if the problem pops up again.