how to remove the unwanted peak in blank sample

Recently we met a severe problem while using agilent 6470 LC-QQQ.

We want to determine the concentration of PFOS, using MRM mode, with the precursor of 499 m/z and product of 99m/z. The mobile phases are methanol and 5mM ammonium acetate in 10% methanol.


The problem is: after one month of testing when I injected blank samples (MS grade methanol or MS grade water), I always get a stable and big peak which has the same retention time as my target compound. The concentrations of my calibration samples are from 50 ppb to 1000ppb and their peak area is from 2.1*10^6 to 9*10^6. However, the peak in blank samples also varies from 1.9*10^6 to 2.5*10^6, which seriously interfere sample testing process.


I tried to remove this unwanted peak: 1. Run mobile phase for 5 days to clean the system and injected over fifty blank samples to clean the needle. 2. Increase the column temperature from 35 to 50℃ and hold for 2 days. 3. Run blank samples with another column or without a column. 4. Change the mobile phase containers. 5. Clean the spray chamber according to the manual.

However, the problem is still there. The unwanted peak area is always around (1-3) *10^6 level no matter what I did.


Please kindly suggest what I shall do next step.

Thanks in advance.

  • Hi,


    Six suggestions things that might be of use.


    (1) could you switch to Acetonitrile based mobile phase instead of methanol?

    (2) perhaps the HPLC is "contaminated" you could try cleaning the HPLC unit itself using the Agilent cleaning solvent, I can give you a protocol if you like ?

    (3) you could try using a higher grade MeOH, like something used for a QTOF MS.

    (4) are there any other MRMs you could try for PFOS that don't product a signal in the blank, we typically use 2 MRMs per analyte of interest, sometimes 3.

    (5) could you try a completely different column chemistry, C18 if not being used already, or Biphenyl, or PFP if using C18 now. Agilent and Phenemonex have good PFP columns.

    (6) Could you adjust your gradient to a very fine increase in mobile phase B to try separate out the interfering peak, assuming it's not something in the MeOH itself.


    Good luck!

  • Hi,


    You may have already solved the problem, but I recommend this Agilent application note:


    PFOS and other PFASs can originate from within the system itself. You can replace a lot of the pump components to reduce the background, but it may be easier to use a delay column after the pump mixer as described in the application note to separate the background peak from your analyte peak.


    Hope that helps.

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