TargetLynx no longer processes certain compounds after changes are made to the MS acquisition method - WKB71844

SYMPTOMS

• TargetLynx no longer processes certain compounds after changes are made to the MS acquisition method
• An empty chromatogram window appears for some of the compounds in the TargetLynx browser

ENVIRONMENT

• MassLynx
• TargetLynx

CAUSE

The function number in the TargetLynx processing method no longer corresponds to the function number in the MS acquisition method.

FIX or WORKAROUND

1. The issue can be fixed by matching the acquisition function number in the TargetLynx method to the acquisition function number in the MS method. However, this may not be an ideal solution if the MS method can be modified again in the future.
2. A permanent workaround is to use Acquisition Function Number "0" for all compound entries in the TargetLynx method editor. The easiest way to do this:
   1. Change the method view via the icon "Toggle view".
   2. Add or select the "Acquisition Func Number" column to the table.
   3. Select "0" in the first row, highlighting the column using a left-mouse click.
   4. Select "Fill Column" using a right-mouse click (see screenshot below).

If the MS acquisition method contains identical MRM transitions (for example, one in function 3 and one in function 25), the latter compound would not be processed. The first compound would be processed twice. To avoid this, change one of the compound m/z values by the second or third decimal place, both in the MS and the TargetLynx method, thereby creating unique entries.

ADDITIONAL INFORMATION

When MS methods are being changed (because additional compounds are added to an existing MS method), the function numbers may change. This will have an impact on the TargetLynx processing method, in which the new function numbers should be altered as well. There is an easy workaround for this time-consuming task. In the TargetLynx method, each compound can be linked to acquisition function number "zero". As a result of this, the TargetLynx processing application will start looking for the compound of interest in function 1, then function 2, and so on until the proper quantification trace is found. The only issue is that when the MS method contains identical MRM transitions (isobaric compounds, isomers...), there is a risk that one of the isomers will not be processed correctly. Instead, the other isomer (residing in the lowest function number) will be processed twice. In this case you can make the identical MRM transitions unique by changing the second or third decimal place on either the precursor or the product ion. You need to alter this in both the MS and TargetLynx method editor. This has no impact on the acquisition of the compounds, but it streamlines the TargetLynx processing.