Hi, I have done a targeted MS2 on a Q-Exactive II for confirming the identity of peak features (metabolomics study), I am trying to find a tool which will give me a parent ion and its fragment in a list, similar to MGF, for all the peaks in the file (example attached), I used a tool called RAW to MGF and it worked only on data dependent files, XCMS is reporting only MS1 peaks, seeMS was the closest but it gives only the base peak for each scan in a list, if I wanted to get the rest of the fragment I had to do it manually for each scan, I wonder if there is any or script which could automate the process, your help is highly appreciated, Cheers, Anas
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