Inconsistent Intensities for Same Sample using a 7890A/5975C GCMS

Hello Everyone,

I am having some issues with my GC/MS and I would love any guidance or ideas that you have. I am currently having an issue where if I run a single sample multiple times (3, 5, 10, etc...), the intensity for each run will vary greatly. I might have two values who are almost identical followed by one high and one low or they may be all over the place. For the most part the retention times are the same barring a few small shifts of a few seconds. This issue has been persistent for a few weeks however it may have been around longer since I am to this job. Below is all of the information I thought was relevant to what I've done so far if anyone has suggestions or would like more info feel free to ask and I will respond as soon as I can. Thank you!

Instrument Info

  • GC: 7890A
  • MS:5975C
  • Autosampler: Gerstel

Method Info:

  • Split or spitless injection (issue occurs in  either mode)
  • Injection volume 2ul (1ul was used to see if amount of sample was too great. It was not the issue)
  • Split Ratio: 1:40 or 1:20 (Both had similar results)
  • Solvent used is DCM (with IS and volatile standards inside having been prepared in MeOH).

Actions Taken to Fix this Issue (Chronological Order):

  • Ion source on MS cleaned according to instrument manual
  • Injection port septa and inlet liner changed and the injection port cleaned with a cotton swab.
  • He gas tank changed as the pressure was very low
  • Removed column from injection port and noticed it had been shoved through ~25 mm which was more than the 4-6 mm recommended. Replaced nut and ferrule on column, cleaned gold seal, and reinserted column 6 mm.
  • Replaced syringe
  • Replaced split vent trap and split vent line.
  • Trimmed approximately 2ft of the column off and reconditioned.
  • Cleaned injection port using a Agilent cleaning method (Scrub inlet with cotton swabs 10x each using Hexane, MeOH, Acetone, and DCM for a total of 40 scrubs.
  • Recalibrated autosampler software as it was ~0.5 mm off when injecting the sample. It would still inject but would slightly jerk to the left when it went to inject.
  • During the entire process, leak checks were performed and none were observed. 

I’m kind of at a loss here so if anyone in this community has some words of wisdom or advice I would greatly appreciate it. Thanks!

  • Your tunes look fine. You mentioned RT shifts, how old is the column ? Any examples of peak shape you can share.? If you take a spectra of the background what are the predominant ions? 



  • Hi Jonathan, I am not familiar with the Gerstel auto sampler but the questions I would ask if you were using the Agilent auto sampler would be what types of rinses of the auto sampler syringe are you doing prior to and after the injection of the sample. Also how may times are you acclimatizing the syringe with your sample prior to injection and how many pumps of the syringe are you doing to remove air bubbles. Does that make sense here


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