timosachsenberg
commented
5 months ago Hi,
General IM support is still a weak spot in OpenMS, and we are happy about anyone that wants to take a lead implementing better support. So right now, OpenMS offers IM support primarily within the OpenSWATH workflow. I recall there have been successful attempt in utilizing ion mobility (IM) binning followed by feature detection through pyOpenMS by some within our community though. I could imagine that the SWATH algorithms can be somehow adapted to MSᵉ but I am unfortunately not an expert here. Maybe @jcharkow or someone from Hannes lab has direct experience with MSᵉ or some hints how this could be approached.
(Digging through our GitHub issues and discussions I can see that there were some developments by Hannes for DDA data, e.g., https://github.com/OpenMS/OpenMS/pull/5829 that unfortunately did not really move forward due to resource constrains. But standard DDA might not be relevant to you anyways.)
ypriverol
Hi, are there any examples of using Ion Mobility data with the FeatureFinder class? Will it account for the additional IM dimension within the RT? I'm looking to extract MS1 peptide precursors and their charge states from full-scan MSᵉ data. Would something like deisotopeAndSingleCharge() be better suited for my purposes?
Many thanks