Hi everybody,

I am recently trying to preprocess my UPLC-QTOF-MS data by MZmine 2 and then export the picked up features to Sirus for identification. My data obtained in Waters QTOF in MSe mode. and they are .Raw files. MZmine 2 is able to process .RAW file though, when I did so, all scans were considered as MS1 scans, so I could not assign MS2 scans to the related MS1 features. When I try to convert the raw files into mzXML as suggested in this website https://envibee.ch/eng/enviMass/topics/PW.php, MZmine 2 seemed able to handle them and there were MS2 scans in the list as shown in the attachment. However, when I used the chromatogram builder and alignment, there were no MS2 data assigned to the MS1 features. I am just thinking if the problem is the conversion of the .Raw file?? Has anybody ever encounter this problem? Or does anybody has some suggestion?

thank you very much

Best regards,

Qi-Zhi Su