7010GC signal drop right after certain peaks


We've had this issue for a while. There is one compound in this analysis. While its RT is at 6.24, there will always be a signal drop at 6.3. The signal drop looks like a negative peak from the base line. 

Here is what we noticed:

In blanks samples: no drop;

Junk peak with same transitions but different RT: no drop;

Different transition but with same parent ion, same RT: same drop;

Different transition but with different parent ion, same RT: no drop;

Other analytes in the same method, different parent ion different RT: no drop.

This figure shows the drop in a bunch of std curves. Two black lines are blanks.

I have also ran a MS2 scan and saw no interference in that 6.3min area. What do you think could be the reason? The flow is 1 mL/min, pressure is 5psi in the beginning condition, column at constant flow. Tune seems ok to me as well (pass check tune and EMV not high <1100, 69 at good abundance10,000,000-ish). Ion source has just been cleaned.

Thank you!

  • How many transitions do you have for this compound?  Could you add more to see what happens to those? For sure include one with no transition - like 154:154 collision energy zero, for example.  You could also do MRM/Scan for that time segment to see the scan spectrum, too.     What is the scale of the chromatogram you shared?

    I wonder if this is hidden underneath a giant mess of stuff in scan mode and you're seeing ion suppression. This isn't broken if other peaks are fine it's just figuring out what's going on...

    7010, so the collision cell gases by default are 1.5 ml/min of nitrogen and 4.0 ml/min of helium.  Some run a 7010 like a 7000 with 1.5/2.25 because they already have the transitions and collision energies worked out and don't want to change them.  The lower helium quench flow will result in slightly higher noise.

  • Hi Paul, 

    Thank you for your reply. This method was not developed by our team. Right now we only have 3 transitions (with one that has no drop and two has drops). I can do a PI and get more. I can do a parent/parent as well Slight smile with 0CE. The scale got cut off in my Qual screen shot. It was 10^3 on the y-axis.

    I thought about ion suppression too. I did a MS2 scan on a std a while ago. I was so sure we would see a monster peak but I got nothing. It was about 2 months ago when I did that. I can run it again just to be certain.

    We are using the default flow. Let me test these and get back to you. Won't be too soon. That instrument is always running Joy 


  • Ella - Try turning off any filtering/smoothing.

    In Acquisition, uncheck these if they are checked.   Advanced Filtering is frequently recommended, but worth trying with it off as a test.

    and from help in MassHunter Quantitative Data Analysis:

    Smooth peak integration

    You can change the smoothing algorithm that is applied to the compounds in your method.  However, applying a smoothing algorithm is not recommended with the parameter-less integrator.

    To change the smoothing algorithm:

    1. If you are not currently viewing your method, open it from Method > Open > From an Existing file . The Open Method File dialog box opens. Navigate to your method and click Open. The Method Edit view opens displaying your method.
    2. If the Advanced Tasks menu is not shown on the left side of the screen, go to the main menu and select View > Method Development Tasks.
    3. From the Advanced Tasks menu, select Smoothing Setup.
    4. In the Method Table, choose the target compound that you want to smooth. Qualifier chromatograms are smoothed using the same parameters as the target compound.
    5. In the Smoothing column choose the type of smoothing algorithm you want to apply to your method from the drop-down list:
      • None (default)
      • Gaussian
      • SavitzskyGolay23 (Quadratic/Cubic)
      • SavitzskyGolay45 (Quartic/Quintic)
    6. In the Smoothing Function Width column, enter the width for the averaged window.
    7. In the Smoothing Gaussian Width column, enter the width of the Gaussian function. This value must be positive and not greater than Smoothing Function Width value.
    8. Validate your method. If you are making additional changes to your method you may complete this step after you complete all the changes.
    9. Save your method. If you are making additional changes to your method you may complete this step after you complete all the changes.

    and let us know!

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