Background subtraction cannot be done for certain retention times

Hi everyone,

I'm running GCMS (5977B MSD) for plant essential oil samples using MassHunter Unknown Analysis. Totally I ran 16 samples, and an error message appeared randomly in 10 samples as " Background subtraction can not be done. The matching background spectrum for the spectrum ' + scan (rt: 4.569 min) was not found. Kindly help me to sort out the issue.  

Thank you

  • Did you import a Quant method? Background subtraction or Blank subtraction?  The help for Quant talks about Background Subtraction and the help for Unknowns Analysis talks about Blank Subtraction.

    This is a very unusual error message.  The retention time is very early.  Is it possible that the first peak starts with the 1st scan in the data file?  As TIC Analysis subtracts the 1st scan of the peak there might be some issue related to that.  

    If there's RT room between the end of the solvent peak and the end of the solvent delay ...reduce the solvent delay 0.05 or 0.1 minutes and see if it happens again.  The other way to get space there is to reduce the initial oven temperature slightly or increase the initial oven time slightly.

    and let us know....

  • Thank you for the reply.

    I'm not using a quantification method. kindly refer to the attached report of a successfully integrated sample.  But when I tried to generate the previously successful reports again, the same error message came with a different retention time  (around 4.03 min), and the retention time kept changing every time when TIC was done in a new window. However, the error didn't appear in a different set of samples of another person run after this incident using a different method. 

    I don't think there is an issue with my samples since the error message came for the C8-C20 alkane standard also. Can it be something like a data crash?

    As per your advice, I will run the samples again next week by reducing the solvent delay time and changing the initial oven temperature.

    I used 80 C as the initial oven temperature and a 50-550 m/z scanning range. The solvent delay time was a common setting at 3 min. 

    Photos of the error messages are also attached.

  • Thank you for those. It might be something much simpler.... what is your acquisition threshold setting?  There has to be background to subtract and if your baseline is data at all...then it can't subtract that.   In your Tea.D data file, zoom way in on the baseline from 4 to 15 minutes or so before the caryophyllene peak...

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