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hadexversum / HaDeX

Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data
http://mslab-ibb.pl/shiny/HaDeX/
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Charge analysis #110

Closed werpuc closed 2 years ago

werpuc commented 2 years ago

To see how the measurements differ between masses, we propose:

  1. mass uptake for different charges and files (distinguished by colors and line types)
  2. plot as for replicates but also with charge info.
werpuc commented 2 years ago

Ad. 1. Mass difference (exp_mass - MHP) in time course for chosen peptide (I selected one with multiple charge values). Separately for biological states. du

werpuc commented 2 years ago

Ad. 2. Mass measured for a peptide in a specific time point with additional information on charge value. This is the same peptide as in the mass_rep previous comment, but in 25 mins.

werpuc commented 2 years ago

I put the charge info on coverage, and I don't have a strong opinion on that:

For all charges at once: cov_z_peptide_all

Charges separately: cov_z_pep_sep

michbur commented 2 years ago

Add the 'Charge analysis subpanel'. The first figure presents the average mass change dispersion resulting from the charge variability (x-axis peptide position, y-axis peptide id, fill: mass change dispersion), the second figure is peptide coverage for each peptide separately and the last plot is the mass uptake for individual peptide. The plot with red line will be added to the replicated bar.

werpuc commented 2 years ago

Code drafts are here. I'll make them into package functions later.

werpuc commented 2 years ago

We should re-discuss it tomorrow, as it is partially solved, but in a different form.

Moreover: There are different charge values for different time points, so I don't how to show that nicely. I noticed, that in no-deuterated samples are more charge values than in measurement - what does it tell us?