ETD Reagent Ion Signal

ETD Reagent Ion Signal brown459  2018-08-08 05:51:56


I was wondering if there were a way to assay the ETD reagent ion signal on a Thermo Fusion Lumos using AutoQC. Currently we look through the individual scan headers output checking the "number of LM found" and the "LM correction (ppm)." This assay requires the instrument method to run Easy-IC. While we have a script that completes this task, it requires a little bit more work than we would like. The reason we want this installed is because we can clean the cathode (ETD source) and restore reagent ion signal when it decays-- increasing our LM accuracy and increasing our signal ETD fragment efficacy. Furthermore, this last point seems to be a great use of the AutoQC system.



Brendan MacLean responded:  2018-08-11 12:21:44

Is this something you can imagine extracting and storing with a Skyline document? If not, then it may be a while before we have a way of opening Panorama AutoQC to support longitudinal tracking of any mass spec related value. Though, it is certainly worth considering, since Skyline already has extendable annotations that can now be imported through a command-line call. I guess we are not far from making it possible to have a script annotate a document and then extending AutoQC to track any numeric annotation.

But, at present, we only support tracking statistics on things you can target with a Skyline document. With little experience in ETD, I can't tell for sure, but checking scan headers doesn't sound like it would apply since Skyline extracts its information from the spectra.

Thanks for your interest in Panorama AutoQC.


brown459 responded:  2018-08-11 13:19:20

I cannot find if there is currently any way to "script to annotate" Skyline documents to do what we specifically want.

Thanks for your continued work!