Plasma reanalysis discussion 19/01/2024

[ypriverol]

We discussed some of the tasks that needs to be done for the plasma proteomics reanalysis project, here is a summary of the tasks:

• Review the list of the projects in the Google Drive.
  • Annotate which projects are outliers from the analysis we did before.
  • Annotate the number of runs and samples.
• Review PRIDE Archive to see new projects that are newly added to PRIDE, for example plasma dataset timsTOFF #246 .
• Review the annotations of the existing projects and fix the following:
  • All plasma datasets -> blood plasma
  • All serum datasets -> blood serum
  • All non-especific datasets -> blood
  • We have to review datasets that are annotated as platelet @asierlarrea
  • Other blood cell types please review EFO ontology
  • Review datasets to get the sex for each sample and other characteristics including disease, age, etc.
• Search for other blood cell types in PRIDE to complement existing datasets (e.g. Erythrocyte).
• Search for immune cell types.