Metabolomics Society Forum

Software => MS-DIAL => Topic started by: FalcoB on March 08, 2021, 09:38:28 AM

Title: MS2 spectra merged or not merged in MSDIAL?
Post by: FalcoB on March 08, 2021, 09:38:28 AM
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
Title: Re: MS2 spectra merged or not merged in MSDIAL?
Post by: Hiroshi Tsugawa on March 13, 2021, 08:07:21 AM
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
Title: Re: MS2 spectra merged or not merged in MSDIAL?
Post by: FalcoB on April 19, 2021, 04:05:21 AM
Hi Hiroshi,

thank you for your reply! Now, it´s more clear to me how MS2 spectra are selected.

Best regards
FalcoB