MS2 spectrum from .mzML file of Waters MSe data

[manohar8]

Hi,
I am able to convert Waters DDA data with MSconvert and same can be processed for IDs using software like Maxquant.
Unfortunately, bulk of the data is in MSe format which post conversion does not annotate precursor in MS2 spectrum (unlike DDA which clearly establishes MS1 and MS2 relationship) and fails in data processing in Maxquant.

Please let me know if there is any way out for this type of data.

Thanks,
Manohar

[chambm]

You can try the DIA Umpire processor to create pseudo-DDA spectra from MS^e. I think we mostly tested it on Thermo DIA spectra rather than Waters MS^e though, so let me know how it goes. Using it is still pretty clunky: you have to give a params file to msconvert (or MSConvertGUI). I was going to recommend you tune your parameters with FragPipe which does have a proper DIA-Umpire GUI, but it looks like MS^e isn't supported there:
Nesvilab/FragPipe#2220

Do you have access to Waters PLGS and Apex3d? I think those are still the state of the art tools for MS^e.

[manohar8]

Thanks Matt! I truly appreciate your response for this query. As you rightly pointed out, DIA UMPIRE does mention about MS^e compatibility, so I will check out, though it might have compatibility issues with current PC config.
The only tool which I was able to find which could establish MS1 and MS2 relationship (at least visibly) for Waters MSe data is Symphony data pipeline (example from a tech note shows spectra for a small molecule) which also works through MS convert but it is a paid software.
Also, I will try to find PLGS download links from Waters website, but that also is not readily available now. It seems proteomics data analysis for Waters data format is indeed limited. Interestingly, Skyline manages to read MS^e data and is able to annotate products ions to corresponding precursors (worked best for a purified protein) but untargeted analysis at proteomic level looks challenging through this route.

Thanks again for all the suggestions.