Ion at every mass


I have a 7890/5975C that has scans that come out like this. This started months ago. I have cleaned the source, inlet, replaced the copper tubing for my carrier gas and checked the manifold many times. My tune report looks normal aside from a bit of moisture. I haven't been able to find any leaks. Multiplier gain is low. Filaments are new. Ions also appear in the TIC as well. Where could this be coming from? I've capped the detector and it appears to go away. Could this be an issue with the electron multiplier? Am I missing something? This is a relatively new instrument to me. 


  • What is the complaint?  The tune shows 166 peaks - a typical number. Air and water are less than 5% of 69 - decent but not perfect. The tune numbers look pretty good. My only worry would be the precursor on 69. I would change the quad polarity to NEG, save the tune file, then tune again and see if the tune ion peak shapes are more symmetrical.

    If you scan lower than 45 you will always see a bit of air/water. Maybe not much, but always some.  The 44 is pretty high, too. 44 is CO2 and is typically a very small percentage, 0.03%.  It is also seen coming from the graphite/vespel ferrule on the transferline.  

    What is your acquisition threshold?   With your current electron multiplier setting and tune parameters it should be maybe 1000.... so that any peaks lower than 1000 are discarded.  That's sort of a typical number/range, too.  

    Do you need to scan lower than 45? Most applications do not need to see peaks of interest with ions lower than that.

    And let us know!

  • My concern is that it also shows up in the TIC. There is quite a bit of noise in the chromatography.

  • What is the acquisition threshold in your method?   With your current electron multiplier setting and tune parameters it should be maybe 1000.... so that any peaks lower than 1000 are discarded.  That's sort of a typical number/range, too.    As the system response changes with time and tuning, the threshold may need to be adjusted to compensate - a typical thing.

  • Current threshold is 500. I am building a duplicate instrument.

  • The EMV setting is probably a bit higher than it was when the method was developed. I would set the threshold to 1000 right now and it would not use the ions below the red line:  If any ions are near the threshold number and go up above the threshold and then down below it, the apparent total ion chromatogram may look like noise even though it isn't.

    And do you really have to acquire data below 45 amu?  If you could change to scan 45 to whatever your current threshold would certainly make for nicer looking total ion chromatograms with lower baseline abundance.

    There's nothing wrong with the instrument or the configuration.  The method needs to  be able to accommodate the minor changes that happen with tunes and system response over time.

  • Need ion 43. Current method scans 40-550. Acquisition method needs to be the same as the other instrument.

  • The spectrum in your picture is down to 10.  40-550 is pretty typical, although there's probably very little response to ions bigger than 400 amu or so.  

    The required threshold will be different on each instrument depending on age, cleanliness, application, concentration of the peaks of interest - many factors - and could even be different on each instrument with each tune if you want to get really down in the weeds.

    Would you be willing to share a chromatogram and a spectrum that shows your worry?  The tune shown above only has 166 peaks in it. A peak at every mass would be >800.  The spectrum shown above is scanned down to 10 with a very low threshold.

    You titled your post as "Ion at every mass" and I don't see it, so trying to help!

  • This turned out to be an issue with the column. I replaced it and the problem went away. Sorry for the late response. Thank you! 

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