Hi, greeting from Thailand, I would like to ask anyone two questions regarding the MSDial software.
1) I am facing a problem with MS Dial software (the latest version), it did not show the MS2 spectra (picture dial4). It does show the MS1 spectra (picture dial5).
I am using Shimadzu LC9030 UPLC-q-TOF/MS with the raw file of .lcd using DDA mode (positive). CE= 35 +- 17 eV. As you can see in picture dial 3, the pink spectra line shows that there is a fragmentation of MS2 right? so I assume that the TOF/MS works well for the MS2 fragmentation.
But when I convert the raw file from .lcd (around 200,000+ kb) using Proteowizard program to be a new file (.mzml) (around 700,000+ kb). or even using the abf converter by converting to .abf (200,000+ kb), by using both ways, the MSDIAL software didn't show the MS2 spectra. The set parameters are showed in picture dial1 &2.
This also happened with every sample also. What should I do please?
2) If the MS2 is still now shown, could I use just the "Peak spot viewer (the ion table)" for the relative quantification result? It shows like w/o MS2: Isosafrole, does it mean that the software has already matched the MS2 spectra of my sample with the MS2 of the library? What does MS2 here mean?