Waters SONAR data conversion for use in EncyclopeDIA

Waters SONAR data conversion for use in EncyclopeDIA david schmidt  2021-05-11


I'm acquiring SONAR data using a Waters Xevo G2-XS. These don't have ion mobility information. They consist exclusively of alternating low- and high- collision energy scans (saved as independent files). Since I can't seem to get good information from waters: What is the recommended way to use these for building chromatogram libraries, for example in EncyclopeDIA?

Thank you very much,


Brian Pratt responded:  2021-05-12

I suppose the question boils down to "how to convert SONAR to mzML so that software that doesn't understand SONAR can use it?"

msconvert author Matt Chambers tells me: "The scanSumming filter will drop the sonar dimension and allow collapsing each retention time (block) into a single profile scan. CWT peak picking should work on it after scan summing. Then programs should be able to treat it like regular MSe data, I think."

I hope this helps!

Brian Pratt

david schmidt responded:  2021-05-14

Hi Brian,

thanks a lot! This support board is brilliant.

Does the scanSumming in msconvert also combine the low- and high collision energy functions, i.e. what happens to the precursor information?

I guess my second question is related to an earlier one by Juan: Do you know whether EncyclopeDIA or other chromatogram library-based software can employ the 1:1 association of precursor- and fragment spectra that waters MSE data provides?

best wishes, David

Brian Pratt responded:  2021-05-14

Does the scanSumming in msconvert also combine the low- and high collision energy functions
No, it just projects all the scans that share the same retention time from (mz,i ntensity, drift_bin) space down to (mz, intensity) space

the 1:1 association of precursor- and fragment spectra that waters MSE data provides
I don't understand the question - that sounds like pretty much the opposite of what MSE does, there's no precursor selection at all. Can you clarify?



david schmidt responded:  2021-05-14

Hi Brian, sorry for the imprecise phrasing.

With the 1:1 association I meant, that for each fragment ion scan (high collision energy), MSE acquires a low collision energy scan which contains primarily the precursor ions. That is quite different for SWATH, for example. I'd expect that having precursors and corresponding fragments in consecutive scans could be valuable information for deconvoluting the fragment spectra. So I was wondering whether this information can be encoded in the mzml and used for peptide identification or whether one should only use the high collision energy function alone?

Regarding the mzml conversion in MSconvert: If all scans with identical RT are projected, will that not convert SONAR data to "All-Ion Fragmentation" MSE data? Then the higher selectivity confined by the window-isolation would be lost.

Thank you.


david schmidt responded:  2021-05-14

As far as I can see, an alternative approach would be Waters Symphony Pipeline for the generation of mzml files.

Brian Pratt responded:  2021-05-14

Skyline certainly deals with MSE data as you would hope ("all ions", in Skyline-speak), but I don't know about other systems.

msconvert emits the low energy scans as tagged as MS1 and the high energy scans tagged as MS2 with a very wide precursor selection, since that's most recognizable to naive readers. In truth they're both technically MS1 scans.

Yes, scan summing SONAR data effectively reduces it to MSE data. Skyline deals with SONAR data but again I can't speak to other systems handling of it.

The original purpose of msconvert scan summing was to allow the use of ion mobility enabled data in systems that aren't prepared for that extra separation dimension, but again Skyline deals with that just fine.

Best regards,