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... 

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