DIANN phospho data configuration

[an-altosian]

Description of feature

Dear team,

First of all, thank you all very much for helping me with configuring DIANN for DIA profiling data. Now, I hope to extend my understanding to DIA phospho data processing. Still, currently I am focusing on DIANN 1.8 because of license. The two major questions I would like to figure out the followings with your help:

1. Do the parameters we all agree with in configuring DIA profiling still apply to DIA phospho data, and
2. What additional parameters are required or should be exposed for phospho data.

For 1, to initialize the discussion, so far we have discussed the following parameters:

1. high speed & low RAM mode: --min-corr 2 --corr-diff 1 --time-corr-only
2. --quick-mass-acc
3. --rt-profiling
4. --no-ifs-removal
5. --relaxed-prot-inf

It will be great if we can confirm they are still needed for processing DIA phospho data.

For 2, the parameters that are special for processing phospho data, I found --monitor-mod most interesting, which will turn on the post-translation modifications (PTM) mode.

Feature request: We might want to add the functionality to add --monitor-mod for variable terms in GENERATE_DIANN_CFG.

TL;DR: From DIANN manual and the DIANN from our internal run, --monitor-mod was automatically added for N-terminal acetylation, phosphorylation and ubiquitination. My questions are:

1. I did not see --monitor-mod specified for any variable terms in the DIANN log for DIA profiling data. Is this turned on only when phospho is specified as a variable term?
2. How can we add this logic into quantms so that --monitor-mod will be added for processing DIA phospho data as in GUI?

Best, Dongze