Ion 44 baseline

Hi! We are actually having some issues with my GC-MS. Some months ago started appearing an annoying ion during all the TIC, the m/z = 44. Some threads comment that could be some air leak. we have checked all the possible parts of the chromatograph and seems not to be that. Also, the autotunes are apparently correct and they do not show me any leak. 

On the other hand, ions 18 (water), 28 (nitrogen) and 32 (oxigen) are very high. I'll attach to this post some screenshots with a blank TIC. The peaks of the blank TIC are due to the m/z = 28 (nitrogen). We want to solve this problem because some peaks appear under the baseline and it is quite annoying.


Thank you for your attention!

Top Replies

  • hello ,


    1) to see when/how the unwanted peaks come:

                   please create an extracted TIC once: Chromatogram > Extract ion chromatogram > type in all masses (18, 28...)



    now we can see if…

  • Do you need to scan that low? Most start scanning at 35. If 44 increases as the oven heats up it is generally a small leak at the detector nut.

  • We start scanning at 40. The ion 44 increases as the oven heats up but we have checked all the nuts and changed it. 

  • Thank you for the answer. We will try it next week! 

  • A couple of questions, Does this system have a purge and trap on it? Is water getting on to the column. 

    The peaks seems to be at coming out at same time interval in the TIC which make me think of something external from the MSD.  I would isolate the MSD from the GC to verify the issue goes away or is still present.

  • You can check it by scanning in the manual tune mode and blowing a can of "air" around the nut or holding a vial of methylene chloride under the nut and see if the peaks spike while scanning. I think the canned air is around 50 for the ion, 49 for methylene chloride.

  • I sometimes get lair eaks from the big O ring that seals the analyzer to the mass spec.  So I try and wipe the seal down with methanol before I turn it on.  Also I have had leaks around the vent valve and we have had to put in a new O ring. 

  • Before you isolate the MSD from the GC, try changing you helium cylinder.  The 44 may be coming from you carrier gas. You can also pull your column from your inlet and plug it with a septum.  The residual gas in the column will be suck out in about 5 minutes.

  • hello


    * vent "valve" O-ring is a consumable, however:
       ~ it ages quickly when dirt particles are pressed in
       ~ normally this O-ring lasts for several years, if it is defective this can also be an indicator: screw is tightened too tight.
          This screw should be hand-tightened + max 1/2 turn


    * the large analyzer O-ring:
       i avoid cleaning the O-ring with solvent
       if my fingers are halfway clean: then i wipe the O-ring with my finger: particels away & regrease the O-ring.
       if the O-ring should have no more grease: use very thin high vaccum grease


    * leaks on these O-rings can be found very quickly with duster or coolant sprays.


    regards, M

  • hello ,


    1) to see when/how the unwanted peaks come:

                   please create an extracted TIC once: Chromatogram > Extract ion chromatogram > type in all masses (18, 28...)



    now we can see if it is a unique entry or if it changes during the run.


    2) how is the inlet EPC set:

          ~ which inlet? (S/SL, MMi...)

          ~ which mode? (S, splitless...)

          ~ which total flow? or is GasSaver on?



            Some inlets, although leak free, tend to increase N2 values if the total flow during the run is very low.

               Simulation: manual tune > SCAN.

                 Now set the total as it is in run mode,

                   if nothing is found: increase the temperature of the GC


    3) For leak search @MSD a spray is mandatory:

          (aero duster spray or) electronic freeze spray down to -45°C (inside ACQ: manual scan: profile on mass 83)

          Then ferrules are not stressed too much, because many users have already destroyed the MS transferline by preventive "over" tightening.


             typical spray (hopefully this will not be seen as advertising here ;-) ) 


    regards, M

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