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MS2 spectrum missing peak information

Dear MS-DIAL developers,

I have been working with both MS-DIAL and MZmine2 for analysis of a DDA dataset (ESI-LC-MS-MS with Q Exactive) as I have run into some confusion regarding the MS2 peak information. In the figures attached, you can see the MS2 of the same compound as displayed by both programs, however, there are many peaks absent in the MS-DIAL image and those shown are not the most abundant as seen in the MZmine2 image.  Is there possibly a setting that I have overlooked or incorrectly applied that would eliminate/obscure these peaks? Or is it possible that there is an issue during conversion of the .raw to .abf that may have happened? I have this issue for all my MS2 spectra of interest.

Thank you for any help you can offer,

Larissa


Re: MS2 spectrum missing peak information

Reply #1
Hi Larissa,

I haven't used MS-DIAL or mzmine2 enough to give you definite answers about the software.
However, I do see that the precursor masses are different between the two images. Not by much, but enough to suggest that they aren't showing the same DDA product scans. I assume this is why they differ i.e. they are showing different scans at different retention times -> different abundances of coeluting peaks.

If the software is showing the 'best product ion scans' that match a library, the difference would be in how they have implemented spectral similarity. There are many parameters that can be tuned and I guess the authors have settled on slightly different ones.

I hope that helps.
Cheers,
Corey


Re: MS2 spectrum missing peak information

Reply #2
Hi Larissa,

as Corey wrote, I am wondering if the two pictures showed the spectra of same precursor ion or not. (The m/z in mzmine may be the m/z of base peak, so of course, you might post the correct pictures.
I hope that the following information helps your analysis.

In fact, different software programs will assign different MS/MS information to precursor ion.
Several MS/MS spectral records will be obtained for each precursor peak from the peak left edge to right edge.
At least in MS-DIAL, an MS/MS spectrum having the highest base peak intensity is assigned to a detected peak.
And in the alignment result, one representative MS/MS spectrum will be assigned to each alignment spot by the following criteria (this is also true in GC-MS project).

(1) an MS/MS spectrum that has the highest spectral matching score among biological samples will be assigned.
Note that the peaks having 'w/o MS2: ' tag will be recognized as "unknown" in this procedure.
(2) If no annotation is existed in all biological samples, an MS/MS spectrum that has the highest base peak intensity among biological samples will be assigned.

Thanks,

Hiroshi

 
 

Re: MS2 spectrum missing peak information

Reply #3
Hi,

I agree that from Larissa's screenshots it can not be ruled out that MZmine and MS-DIAL are showing different spectra. However, in case of MZmine the spectrum can be traced back to file "141.mzXML" spectrum #1873. Is there a way to show such precise origin of the MS2 spectra in MS-DIAL? I hope this could help to settle the issue.

Best,
romas





Re: MS2 spectrum missing peak information

Reply #4
Hello,

Thank you all for your insight. Indeed, the spectra originated from different scans. Scan #1873 in MZmine is the desired spectrum however, for the spectrum of 564.33 m/z in MS-DIAL, it originates from scan #1886 (peak spot view of file 141; See attached images). According to MZmine, scan #1886 has a precursor of 282.2527 m/z, not 564.33 m/z. Is this an example of how the programs differ in the assignment of MS/MS spectra to precursor ions as describe by Hiroshi? Are there parameters in MS-DIAL that I can change that will result in more/different assignments? There is only a single peak spot for m/z 564.33.

Thank you again for your expert advice,

Larissa

Re: MS2 spectrum missing peak information

Reply #5
Hi,

the scan number that you find in ms-dial does not have the same meaning as in mzmine.
I have an idea. Did you start your project as "profile" mode in the start up window of MS-DIAL? or did you start it as "centroid" mode?
If you start with "profile mode" for both ms1 and ms/ms, can you try to restart your project by selecting "centroid" for both ms1 and ms2?

Thanks,

Hiroshi

Re: MS2 spectrum missing peak information

Reply #6
Hello Hiroshi,

Thank you very much, that fixed my issue! I had changed MS2 from profile to centroid, but I had not done MS1. When I set both to centroid I now have a recognizable spectrum.


Thank you for your quick responses and dedication to fixing this issue!

Larissa