Hi Christopher and Matt,
If you are aiming for maximum coverage I would not advise using DIA-Umpire since it cannot support IMS information and the best results in identification (and quantitation if you are aiming for low abundant peptides) are obtained when you perdorm IMS-MSE (a.k.a HDMSE) experiments. I tried DIA-Umpire with some MSE files and the results were poor to say the least, but it could be I didn't find the optimal settings and didn't invest enough time into it.
That I am aware of, only Apex3D can support the data deconvolution of Waters data containing IMS information. Apex3D is a subprocess that is run prior to searches with PLGS to generate the pseudoMSMS spectra of features alligned in the RT and ion mobility dimensions.
From the PLGS software you can export the .mgf files generated by Apex3D to perform searches in other search engines if you prefer. Personally, I prefer searching the .mgf files in other search engines because the output of PLGS ("*_final_fragment.csv" files) only shows the matched fragments, making you essentially blind to all the other signals present in the allignment that might be important in confidence assignment of the peptide. The problem with the .mgf output of PLGS is that it performs charge deconvolution both for the precursor and fragment ions (I assume to facilitate identification) which would prevent you from mapping back the identifications back to the raw files to generate the EICs.
Alternatively, you can run Apex3D from the command line to generate the .mgf files as input (e.g. for MSAmanda on Skyiline) without applying charge deconvolution to the precursor ions. However, we haven't found a way to not apply charge deconvolution to the fragment ions so any multiply charged fragments that have been deconvoluted would be missed.
Finally, Apex3D also generates a "*_Pep3D_Spectrum.xml" output that contains all the binned information necessary (i.e. alligned ions dected in the low energy, high energy scans, and same IMS bin (if used)) to generate the pseudoMSMS spectra. However, a parser would be required to extract the information.
By the way, Skyline supports Ion mobility data from HDMSE files generate from Synapt G2-Si instruments! It is beautiful to finally be able to visualize the real data instead of relying on the PLGS and other Waters supported blackbox softwares.
Hope this information helps somehow.
Matt, if this topic moves forwards I would be more than happy to provide access to data related to these topics that we have collected and curated if it is needed.