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Thermo Fisher Scientific

How to determine whether the noise is chemical noise or electronic noise in the Ion Traps


Ion traps experiencing unexpected noises.


  • LTQ Series
  • Tribrid Series


To determine if the noise is chemical:

  1. Turn off the spray voltage and possibly any liquid flow through the spray needle.
  2. If the noise goes away, then likely the noise is chemical.
  3. Flush all lines and the source chamber including the probe.  
  4. Replace the ion transfer tube. (Chemical noise is rarely due to contamination inside the instrument since there usually isn’t enough ionization present inside the vacuum to generate new ions to detect.)

NOTE: Finding the source of the chemical contamination is mostly beyond the scope of this document.  It is useful to confirm, however, that the calibration solution is not contaminated (if the noise is present during calibration) by using a different bottle of solution, if available.


If the noise is still present after stopping the spray, then the noise is likely an electronic noise. Chemical noise will also usually be characterized by being at specific m/z values and will also likely have an isotope distribution consistent with a normal chemical composition. If the instrument is either a Tribrid or an LTQ Orbitrap, the same m/z ions will be present in the Orbitrap.

NOTE: Special case of chemical related noise: APCI chromatogram shows a lot of noise, but only at the end of the run, during high organic elution.

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