Retention time for spike-ins

mpc-bioinformatics / McQuaC

Transform the Quality Control workflow from Knime into a workflow in Nextflow

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Open KarinSchork opened 3 days ago

KarinSchork commented 3 days ago

give retention time (and maybe total RT duration) in minutes instead of seconds?
retention time delta column can be confusing, especially as expected retention times are hard to determine

julianu commented 3 days ago

Do we generally use minutes? Maybe wait until the mzQC hackathon and see, whether there is a defined unit.
total RT for the spike in? This is not monitored right now, or is it?
Hm, I was under the impression that exactly the delta would be the most interesting between the runs, as it directly shows you the shift from the expected value

KarinSchork commented 3 days ago

we use seconds but @SvitiMPC said they use minutes all the time in the lab and it may be more intuitive
there are the columns SPIKE_MPCSPIKE2_MZ_895.9493_RT_4212_RT_at_Maximum_Intensity and the delta is the difference between that and the expected RT
I think the problem is that the expected RT cannot really be set accurately, especially when gradients change.