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Topic: MS2 spectra merged or not merged in MSDIAL? (Read 152 times) previous topic - next topic

MS2 spectra merged or not merged in MSDIAL?

Hi,

for metabolomics analysis we record our MS2 spectra in DDA mode on a QTOF device (TripleTOF 5600, Sciex).

Especially in the case of pseudo molecular ions with higher intensitites we sometimes get up to three single MSMS spectra per feature and file.

Now, my question is: Are these different MSMS spectra are merged during data processing in MSDIAL? If the spectra are not merged and you have let´s say e.g. three MSMS spectra per feature and file, which of them is then used for database annotation?

Regarding merging, I did not find any setting options in MSDIAL yet (e.g. MS or Rt tolerance). But from my experience I know that merging of MS2 spectra is possbile e.g. using vendor-specific Sciex Software (PeakView) or R/XCMS.

Thanks for help!

Best regards
Falco

Re: MS2 spectra merged or not merged in MSDIAL?

Reply #1
Hi Falco,

only one MS/MS spectrum is assigned to each precursor ion even though the multiple spectra are acquired in the experimental data for a precursor peak.
Currently, from the left to right edges of detected peak, the MS/MS spectrum having the highest basepeak intensity is assigned.
For the representative spectrum for alignment peak spot, see below.

http://www.metabolomics-forum.com/index.php?topic=1388.msg4061#msg4061
http://www.metabolomics-forum.com/index.php?topic=1396.msg4123#msg4123

Thanks,

Hiroshi