Recommendations for Proteomics

Proteomics studies are used to find biomarkers for disease and susceptibility.

Repositories

For a curated list of relevant repositories see FAIRsharing using the query ’proteomics’. The ProteomeXchange Consortium enables searches across the following deposition databases, following common standards.

• For shotgun proteomics use PRIDE
• For targeted proteomics use Panorama or PASSEL
• For repossessed results use PeptideAtlas or MassIVE

Data and metadata standards

For a curated list of relevant standards see FAIRsharing using the query ’proteomics’.

• Use the minimal information model specified in MIAPE by the HUPO Proteomics Standards Initiative (HUPO PSI), and fill the model using the controlled vocabularies specified by the Proteomics Standards Initiative, PSI CVs
• Recommended formats:
  • For gel electrophoresis gelML
  • For transition lists TraML
  • For raw spectrometer output mzML
  • For reporting mzTab
  • For protein quantisation data mzQuantML
  • For protein identification data mzIdentML
  • For metadata ISA-TAB with conversion to PRIDE format