Profinder time alignment reference keeps changing..


I am conducting untargeted analysis, and use Profinder for recursive molecular feature extraction. Before that, I always run "Time alignment" and use a pool sample (mixture of all samples in that batch run) as a reference. But recently, I noticed when opening different profinder file (saved for different batch runs or experiment), the reference chromatogram keeps changing to the previous one.

I am wondering if it is better to create a method for each profinder file. Because I have been using a one method to process all my profinder files (since running for same parameters: e.g. s/n ratio 5 count 7k etc) But for each profinder file, I always select the reference sample/chromatogram to the one in the same batch and do the time alignment before processing MFE. 

But it feels like it is showing the reference chromatogram is keep showing the previous one (which is from a different batch run) whenever I open a different profinder file... 

  • I believe this doesn't affect the overall MFE results. If I do the time alignment again, of course, I will have to process the MFE again.

    But FYI - I double-checked and realized it shows the reference chromatogram I selected in the method I was using. For example,

    (1) with the method A , I picked a REF1 for time alignment in Profinder File 1.

    (2) Later I processed Profinder File 2, picked a REF 2 (totally different with REF 1) for time alignment, then processed the MFE with the same method A. 

    When I come back to check Profinder File 2, it opens with method A and the reference chromatogram for time alignment is not showing as the one I actually used (REF 2) but shows as REF 1.

  • Hello  ,

    I apologize again for the delayed response.

    I have been able to confirm that the reference chromatogram is stored as part of the method. If you load a method, change the reference chromatogram, and then process the project, it will use the new reference chromatogram. But that is not saved as part of the project.

    Best practice would be to save a new method for each project, even if all the other settings are the same. This will allow you to easily see what reference chromatogram was used, though you will need to load the method if you go back to a previous project. 

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