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Published 20 hours ago • verified publisher icon OpenMS

IsobaricQuantifier MS2/3 error handling

Open jpfeuffer opened this issue 1 year ago • 1 comments

If you specify "select_activation" to e.g. CID but you are using an SPS MS3 TMT experiment where all MS3 scans are beamtype CID, you will just get non-sense results because it tries to quantify the MS2 only.

Maybe warn or better even fail when MS3 scans are present but none of them match the given activation? Other suggestions? @cbielow @timosachsenberg

See also https://github.com/bigbio/quantms/issues/320

jpfeuffer avatar Oct 30 '23 15:10 jpfeuffer

Can we find out what other software is doing here? e.g. is it reasonable to assume that the highest HCD level is used for quant?

timosachsenberg avatar Oct 30 '23 16:10 timosachsenberg