What needs to be done for the manuscript

[mlocardpaulet]

To do:

• We need to make sure that the documentation is correct and up to date (see Merging documentation and description on website #344)
• The raw and intermediate files should be available for download to the community (see search results accesible for download? #316), and edit documentation accordingly (see write documentation on how to retrieve the intermediate files, data points, etc... that we store #174)
• Do we want to actually implement a reviewing process for module proposal? -> NO, discussions are enough.
• What do we want to discuss regarding DDA quant module in the paper?
  • different versions of the same tool do not output the same results
  • same tools same version can output different results due to a random step (MQ)
  • MBR increases coverage (detection across replicate runs) with a cost: reduced accuracy
  • 2nd peptide search with MQ?
  • there is kind of a linear trend: higher sensitivity ~ loss of ratio accuracy
  • What parameter sets/tools are missing?
  • Do we want to dig deeper (look back at the raw/intermediate files) and if yes -> what do we want to investigate?
  • check public data sets in the DDA quant module. Are these correct? (I have doubts on the FragPipe outputs, I may have messed up there)
  • check what tools we are compatible with in the DDA quant module. Decide how we want to handle Proline (there are many different outputs due to the flexibility of the tool) (see Full support all software ion module #346)
• Do we want to discuss the peptidoform module? (I think that it would be nice to advertise WOMBAT-P and see if the results are different from the DDA quant module).
• What do we want to discuss regarding the DIA module?
• We should discuss the opportunity for collaboration within the community initiatives: examples with WOMBAT-P and the de novo benchmarking module https://github.com/orgs/Proteobench/discussions/356.
• write material and methods
• automatisation using jupyter notebooks?