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PNNL-Comp-Mass-Spec / Informed-Proteomics

Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data
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EThcD activation type #11

Open AaronStorey opened 6 years ago

AaronStorey commented 6 years ago

Which activation type is most suitable for EThcD fragmentation, which generates both c/z- and b/y-type product ions? Thank you very much.

FarmGeek4Life commented 6 years ago

The current automatic handling of fragmentation types (what happens if you specify "Unknown") defaults to ETD for ETciD and EThcD. If I remember correctly,we decided on this because the primary fragmentation is ETD, and the primary purpose of the supplemental CID or HCD is to complete the fragmentation started by the ETD, so the ETD scoring models more closely match EThcD/ETciD. Beyond that, we haven't done testing on EThcD/ETciD data to see the effect on results when it looks for both c/z and b-y ions.