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Topic: Please help ... Asking about the MS/MS spectra is not acquired in MSDIAL (Read 290 times) previous topic - next topic

Please help ... Asking about the MS/MS spectra is not acquired in MSDIAL

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?

Looking forward to your kind answer :)
Nuti

Re: Please help ... Asking about the MS/MS spectra is not acquired in MSDIAL

Reply #1
Hi Nuti,

I asked Shimadzu persons who use MS-DIAL program, and they may answer your questions as well.
My understanding for Shimadzu 9030 QTOF is to export your data as mzML in LabSolution software. Then, the mzML format can directly be imported in MS-DIAL program. Did you try this?

For your second question, see http://www.metabolomics-forum.com/index.php?topic=1580.msg4749#msg4749

Thanks!

Hiroshi

Re: Please help ... Asking about the MS/MS spectra is not acquired in MSDIAL

Reply #2
Hi Nuti,

I received several comments from Shimadzu persons. They also recommended to use LabSolutions software to make mzML files as attached. If you still have some troubles, please let me know, and Shimadzu and I can help you.
Thanks,

Hiroshi