Protein inference module: from peptidoforms to protein groups

[mlocardpaulet]

aim of the new module

1. what is its aim?
evaluate software capability to summarize peptides (or precursors)-level quantities into protein-level quantities. This module would be specifically focused on this step of the analysis, so it would provide a peptidoforms (or precursors) matrix as input. This way the summarization would be done on the exact same input.
Users would submit scripts (could be R or Python, if possible to have multiple language compatibility). And we would run the script directly on the input data that ProteoBench proposes 
The output could be a matrix of protein-level quantities. This, way, we could run easy summarization algoritms (mean, median, sum..., and/or use packages with more complex designs such as MSStats, MSQROB). The script could include missing value replacement, normalisation etc... 
2. what is its added value compared to already available modules?
a) there is no module for protein inference/summarization only yet. 
b) I think that this system of having a script as input could be useful for other modules. It could be the first of many modules based on script submission.

full description of the new module

I am actually not sure if this is feasible. Scripts may require different packages, I am not sure if we can run any script easily. But I think that it is worth thinking about it?
Other challenge: how can we parse the script to get the set of parameters of interest that we could show on the module results?
Regarding data, we can easily start working with some output from the current HYE modules, but I think that it would be more interesting to work with something a bit more tailored to challenge protein inference: sample with multiple isoforms? 
We could also use simulated data (a matrix of tryptic peptides from a set of regulated proteins).

potential external expert(s)

I don't have anybody in mind yet, I am just opening the discussion.

Will you be able to work on the implementation (coding) yourself, with additional help from the ProteoBench maintainers?

• yes
• no

any other information

...