Ion Ratios – How the range is calculated in the Methods, with added twist in TF 3.3

TraceFinder has 4 functions for ion range calculations.

Ion Range

1) Manual – This functions as the name implies, it allows the user to define a targeted ratio by manually entering it in the ratios section of the detection tab of the confirming ions of a compound.

2) Average – This functions allows the data to drive the targeted ratio of each confirming peak by averaging the detected peaks for each confirming ion in each component from the calibration curve and applying the average as the target ratio. This is useful in many clinical experiments where response may be variable across sample sets.

3) Weighted Average – Performs the same function as Average with the exception that it weights the bottom end of the curve in the calculation of the target amount. This is useful in assays where the expected amounts in the unknown sample types are typically on the lower end of the calibration range.

4) Level – This selection allows the user to select a level from the calibration curve as the target ratio reference. In some labs the SOP’s  require that a specific calibration point be compared for the batch of samples.

The selection of 2-4 are widely used in the applied markets. This relieves the use of having to perform the calculations manually outside of the application and then hand entering the data.

Also to note is that if you are working in a batch of samples such as a verification samples set. You may use settings 2-4 to calculate the values then changes the setting to manual. This action keeps the calculated value in the target field. you can then update the Master Method template and use these ratios for all validated batches to follow.

TraceFinder 3.3 has the benefit of being able to store the ion ratio criteria in the Compound Database so that you may perform quick holistic edits or use the same criteria in different assays without recalculating the values and manually entering them. As with the methods themselves, each ratio has properties that can be set as:

  • Window Type – How to calculate the width of the range around the target ratio
  • Ratio Window – The amount of the range
  • Coelution Value – The amount in time that the peak apex of the confirming ion can be different from the quan peak.


The file hyperlinked below is an example CSV file template for a compound database for TraceFinder 3.3. This file will allow you to record settings from other methods. If you are transferring from one instrument platform to another, this enables you to quickly create the same method in TraceFinder.

Click here to download the ZIP file -> Default

As a reminder TF can group in the CDB and the Method up to 6 components as individual integrated quantitative peaks under the compound name. This allows the peaks to be viewed and manually manipulated individually in data review but the responses summed as the total response of the compound. Each of the 6 quantitative peaks may have up to 10 confirming peaks with individual ratios and ranges.  (A key note is that the Quantitative peaks need NOT be coeluting. (ie.. Chiral compound analysis)) This feature is mostly when using GC EI experiments or LC experiments with multiply charged components.

About humphrjk

Product Manager for Analytical Software for Chemist. Analytical Chemist, Mass Spectrometry Scoutmaster Troop 4277 Skipper Ship 4277 Vice Commodore Texas Sea Scouts

Posted on July 12, 2015, in Ask a guru answer, Method Development, TraceFinder 3.3, Tutorial and tagged , , , , , . Bookmark the permalink. Leave a comment.

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