We have Shimadzu LC MS/MS with Lab solution software. Now the file is exported to MZXML in 'Centroid' and then converted to MZML by using MSConverter. But now not able to process it in MSDIAL, showing peaks are not found. what should we do to process?
Hi Anish,
I agree with Qi-Zhu Su's response above, BUT before you do that do check a few things:
1. Check that in the Lab solution software you do see MS/MS spectra and that you have acquired MS/MS data.
2. The in the MSConverter make sure that in the peak picking you have MS Levels 1-2 specified and other settings as you can see in the attachment!
Hope it helps.
Thanks,
Biswa
Thanks @Qi-Zhi
Biswapriya Biswavas Misra Hii, thank you for the response. However, I tried and also able to directly export from the system as MzML. But now the issue is when I was trying to run in MS Dial it is not able to detect MS2, the library also showing as "w/o MS2". I am attaching a file of snapshots also, can you pls help?
Hi,
On the software, instead of "suggested" CHECK on "MS2" and see if you get anything in the "spots" or "ion table". If NONE, then your data does not have MS2 for the following reasons:
Raw to mzML conversion issue by MSConverter/ Shimadzu tool.
or, the equipment settings used did not generate any MS/MS.
More likely that the later is true!
Btw, in MS-DIAL software the "suggested" = "w/o: MS2" where just based on MS1 mass accuracy it allows certain matches at a given mass tolerance. These are mostly unhelpful and can not be trusted without MS/MS.
Thanks,
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