Unstable TIC in MS 5977A

m/z 207 is usually column bleed, only way to get rid of it is to not run the oven up to 280

It shows that your column 1 flow is 3.0 ml/min.  The optimum hydrogen carrier flow into the orthogonal ion source is about 0.75 ml/min. The pumping capacity using hydrogen is about 1/2 that of helium so lower total flow is required, your flow must be lower.    Please share the last autotune report.

And for running hydrogen carrier gas, please see:  user-guide-coverting-ei-gcms-instruments-5994-2312en-agilent.pdf, Switch to Hydrogen or Nitrogen as Alternate Carrier Gas ,  Agilent  flyer-hydrogen-safety-lab-use-5994-5871en-agilent.pdf   .

Hi Paulsalverda, thank you for your response. We installed a guard column in our GC, and that 3.0 mL/min is the flow rate in the guard column. The flow rate into the ion source is set to be 1 mL/min. Here, I provide more detail about our GC:
The source we are using is Inert EI 350 and we use 6 mm Drawout Plate. The reason is because we still want to operate this GCMS under H2 and He carrier gas without having to vent the system. Another thing I noticed from the recent Tuning Report is that the ratio of 219 to 69 is slowly decreasing from 80% to ~69%, and the EM voltage is increasing from 1800 to 1930 (I attach the tuning report below). Could it be an indication that our ion source is dirty?

What confuses me is that sometimes that TIC fluctuation disappears (like recent runs) and the TIC looks fine and normal, as well as the Atune report. I'm just wondering, have you ever seen these symptoms before? if yes, what is actually the root cause of this? Is it considered as a high background noise, or does our ion source have a problem?

Thank you.

Thank you for your response. Yes, we have to go up to 280 because we are analyzing hydrocarbon samples. But, we are more concerned about the spectrum that spans from 50-550 m/z as in an ideal run, this does not happen. 

As soon as a clean ion source is installed into a GCMS it starts becoming contaminated. Everything that comes out of the column goes into the ion source. PFTBA goes into the ion source. The adhered sample residue on the source radiator, quad radiator, quad, detector, and vacuum chamber continuously redistributes. All of this means the ion source will need cleaning. The more samples that are run, the more tunes performed, the sooner it will need cleaning. 

Is this what you are calling TIC fluctuations?  What is the raw abundance of this?  Can you share a data file so we can see the scale of the chromatograms?

This is from the tune. That large peak is either 40 or 44... Argon or CO2.  This should not be there.  Is your gas contaminated?   44 can come from the graphite/vespel ferrules, too, so how long has it been since the transferline or Capillary flow device ferrules have been changed?

Please share the acqmeth.txt file that is located in the data file windows subdirectory  -- so under \GCMS\1\Data\Reducing1.D and also detail the exact physical configuration of the guard column and analytical column. How are they connected?  Are you using a splitter or purged ultimate union?