Hi,
I m working with a 5977B GCMSD and since several days i ve got a absence of noise (see image) Scan Mode Atrazine analysis.
I m very embarrassed because i want students to define S/N ratio and of course S/N ratio calculed in absence of noise gives me a infinite ratio !
Is anyone i ve an idea of this problem.
All tunes are fin, no pollution.
Thanks a lot.
In your MS Method, if the Threshold is set higher than any baseline/background ions then the baseline will go to zero as all ions are rejected. The Threshold needs to be enough to reject the electronic background, about 50, and is often set much higher to reduce the number of background ions from column, air, contamination, or caused by high gain/EMV settings.
This chromatogram shows this by the drop off at the end when the signal for this extracted ion goes below what looks like 200 counts rather than tailing off smoothly to baseline.
Try reducing the Threshold. That should not adversely affect your calibration. Or you could increase the EM gain to drive higher baseline and bigger peak heights but that will certainly affect your calibration.
This also happens if the run method is not pointed at the current autotune file and the actual as-run MS parameters are not as expected.
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Here the results after changing Threshold values 10, 50 and the last 5.
These are very small peaks, which is much better than too large! These are extracted ion chromatograms so for any individual ion there is always a chance of no background, especially above about 150 amu where there is less background normally in GC/MS. To increase the baseline signal you'll need to increase the run's Electron Multiplier Voltage in each method used.
There are three ways to do this.
During autotune the algorithm creates a gain curve for the EM. Acquisition uses a number to access that curve from 0.05 to 25, less than autotune up to much higher than autotune. If you are currently using Gain 1, for example, try Gain 5. Note the Applied EM voltage change between Gain 1 and Gain 5. Make sure that this increase doesn't make the high standard peak height too big. The maximum abundance per ion on single quad instruments is approximately 8.4 × 10^6. To stay within the linear range of the electron multiplier, make sure all ions are at or below 2.0 × 10^6 . (see: Optimizing Detector Gain 5991-2105EN, March 22, 2013 )
Delta EMV allows you to set an arbitrary voltage offset from the current autotune EMV. So if the tune EMV is 1109V, you could enter +200 and the run EMV would then be 1309V. The issue with using this is that the EMV, and so the signal level, will be different after every tune.
Absolute EMV lets you choose an arbitrary EMV setting. So you could choose to run at 1309V forever. The issue using this is that it does not compensate for source cleanliness or EMV aging over time.
Or, you could extract more than one ion from Atrazine (200, 202, 215, 217, 173) and do the S:N on their combined abundance. You could also use the TIC or change your method to run SIM.
