Low Sensitivity in LC/MS due to High Background

I have an Agilent LC/MS Ulitvo TripleQuad and overnight it seems as if I have lost complete signal of my peaks. Sensitivity has dramatically fallen. A technician confirmed that our MS was fine and that the background was extremely high when just running normal water and methanol (MS grade) through the instrument. They are hypothesizing that there might be salt build up throughout the instrument. I normally run my method on a gradient of 10mM Ammonium Acetate in UPW (Mobile Phase A) and 10mM Ammonium Acetate in MeOH (Mobile Phase B). All solvents used are MS grade and run on ESI + mode.
I have tried flushing the system but still see the high background. Does anyone have a suggestion for flushing out Ammonium Acetate or reducing high background in LC/MS?
Or any possible hypothesis for what the underlying issue could be? It seems to have dropped ins sensitivity overnight. I would think the signal would slowly get worse if there was a buildup of salts overtime.
Thanks in Advance!
  • HI Katie, 

    Would you be able to upload a screenshot of the contamination you're seeing? Or list the contaminant ions? 

    I regularly run 20mM and occasionally 200mM ammonium acetate into my QTOF for years and I do minimal cleaning so I don't think that is the source of contamination unless it was a poor grade.  

    A good general cleaning solvent is 50% IPA:Water + 1-2% acetic acid (I occasionally go higher). I don't flush into the MS though. 

  • Hi Katie,

    Did you solve the problem or not yet, i would like get in touch with you because i have the same troubleshoting right now which i lost totally the signal and i have a very high background.

    could you please tell if your problem persist or you succeed to solve it.

    Thank you in advance.


  • Hi Houceine, 

    What grade/manufacturer of of AmmAc are you using? And are you in the same solvents as Katie? 

    Do you see buildup on your source? 

    Also, if you are adjusting your pH, what acid are you using? (had a few customers use things like hydrochloric acid in the past, which generates insoluble salts)

  • same as katie, but i don't see any buildup on my source, besides i clean the source several times and still have the same problem, the background too high (almsot 40 millions) and nothing appears with any of my studied compounds.

    for my pH in my protocol no needs to adjust ( working with acidic medium). also all the used solvant or comound are LCMS-grade.

  • Would you mind sharing a screenshot with the background and masses? 

    And do you mind saying what the brand/part number is of you ammonium acetate? Hopefully there's not a bad batch out. 

    I'm using Supelco's Lichropur LC/MS (5.33004) for any of my direct infusion work but I have also tested Acros and Supelco Lichropur HPLC grade (5.43834) by infusion and it's almost as good so I use it for 2D-LC (SEC/RP). All of these gave low background at ~200 mM. 

    Do you see the background if you run normal ACN:Water:0.1%FA? 

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