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How do I determine my Minimum Intensity Threshold (MIT) value in FractionLynx? - WKB5474

Article number: 5474


Determine the Minimum Intensity Threshold (MIT) value in FractionLynx.


  • FractionLynx
  • AutoPurification
  • Fraction Editor file


To manually determine the MIT:

  1. Make a blank injection of a solvent that is representative of the sample diluent.
  2. From the Chromatogram window, open the chromatogram of the blank injection.
  3. Display the target traces of the extracted wavelength or mass that is targeted for fraction collection. Be sure to display any additional adducts.
  4. If the baseline does not drift significantly, use the signal intensity value in the upper-right-hand corner of the extracted chromatogram to determine the MIT value. In the example below, this value is 7.75e3 or 7750.


Determining the minimum intensity threshold:
To avoid collection of undesired fractions, the MIT must be set to a value greater than the intensity of the background of the detector. Different detectors produce different background intensities. Different masses and wavelengths can produce different background responses, and these values vary over the course of a run due to solvent changes.

You can determine the background responses for each detector from a blank injection, and then set the MIT accordingly by following this procedure:

  1. Open a chromatogram that contains the compound that the customer wants to collect.
  2. Zoom in on the peak of interest.
  3. From the command bar, click Edit > Copy Chromatogram List then click Edit > Paste.

A box will appear that contains the chromatogram view in text format where the intensity is shown for each data point on the time axis visible in the window.

  1. You can pick an intensity value for the baseline or a bit higher on the peak. You can also paste this information in notepad or excel for easier viewing. The command copies the chromatogram in an ASCII format.

In order to prevent false triggering, the MIT must be set higher than the background intensity of the extracted mass spectrum. The average background intensity of the blank in the example above is approximately 7.75 e3 or 7750. The background intensity for this single mass is typically multiplied by some factor, such as 10, 50, or in this example 100, to ensure that the MIT is set high enough to prevent false triggering for all the masses. This value is entered in the MIT field of the FractionLynx method.

Exceptions:  Negative MS ionization, UV, PDA, and analog data may use different intensity values for collection.

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