Elution group module

[GeorgWa]

All precursors & their fragments with the same modified sequence.
Grouping variables can be set to include:

Charge states (same RT, diff. IM)

Isotopologous labels (diff RT, diff IM(?))

(same RT, same IM without Deuterium effect)

Different approaches:
Calibration model
Dimethyl calibration: rt(seq) + rt(rt,label)
Use predicted rt difference as starting value

Model free correlation
Align channel elution profiles within subgroup
Fast correlation matrix calculation

Questions

• quantify Deuterium effect
• potentially 1,2 cycles difference
• Is the RT diff independence of the sequence?

Ionization losses (same RT, diff. IM)

Phospho loss during ionization (?)
Ask @jalew188 about relevant losses

Pseudo RT and pseudo IM alignment for different peptides?

Future Ideas

Elution groups across all runs. Elegant MBR

[jalew188]

Now we have discussions on github, we can move these into discussion as they are not issues, see https://github.com/mannlabs/alphadia/discussions

[GeorgWa]

I created them through the projects view. And I think I had to convert them to issues to assign them to a milestone.
AlphaDIA

But I agree. Discussions are be better suited.