Fixing Comet Parameters and Caluclationof Spike In Information

mpc-bioinformatics / McQuaC

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

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Fixing Comet Parameters and Caluclationof Spike In Information #57

Closed Luxxii closed 4 months ago

Luxxii commented 4 months ago

This fixed #55

Also the SpikeIns are now retrieved and reported as discussed:

SPIKE_IDENTIFIER_MZ_XXX_RT_XXX_Maximum_Intensity --> Maximum Intensity of specified RT (corrected if an identified MS2 Spectrum reports another RT)
SPIKE_IDENTIFIER_MZ_XXX_RT_XXX_RT_at_Maximum_Intensity --> The Retention time of the Maximum Peak (from above)
SPIKE_IDENTIFIER_MZ_XXX_RT_XXX_FoundPSMs --> The number of found PSMs, if any
SPIKE_IDENTIFIER_MZ_XXX_RT_XXX_Delta_to_expected_RT --> The Delta, which is always calculated, based on the input spikeins.

KarinSchork commented 4 months ago

It runs through and seems to work, however I would suggest that @julianu has a quick look if the values are now extracted as intended (I honestly lost track a bit during the discussions yesterday)

KarinSchork commented 4 months ago

I found an issue: in my test data, some spike-ins have 0 as maximum intensity and get the same RT (3600, so end of run?) as an RT table0_summary.csv

julianu commented 4 months ago

I am working on this on another branch...

Luxxii commented 4 months ago

Well this makes sense with a maximum intensity of 0 and a maximum RT of 3600.

The SpikeIn was expected to be present at RT ~4220s, however the run was only 3600s. We could handle the edge cases differently if this seems confusing. So e.g. if intensity == 0 --> None (for Maximum Intensity) and if intensity == 0 --> None (for RT ant Maximum Intensity)

KarinSchork commented 4 months ago

Ah I see, so my test files had a shorter gradient, makes sense. I would see it as an edge case then, and set RT to NA if there was zero intensity.

di-hardt commented 4 months ago

@julianu patched the spike-in search and used the retention time from the best spike-in PSMs for the XIC extraction while also restructuring the XIC extraction itself as both go hand in hand. As result we have a bit of an overlap between this PR and the following commit on the restructure branch: https://github.com/mpc-bioinformatics/Next-QC-Flow/commit/4682976a63f1be3d6d30e83a66dafca8750f6da9

I would suggest to pause this PR indefinitely. May be we can delete the PR completely. @Luxxii would you consider to check it, as it is your work/PR.