Summary

  • ProteomeXchange provides a single point of submission for MS-based proteomics data to all public repositories using the ProteomeXchange submission tool. 
  • It is developed by the ProteomeXchange consortium, a collaboration among the groups that develop the main MS-based proteomics repositories.
  • Submitting proteomics data to ProteomeXchange is a simple way of ensuring that your data is made available to the research community and propagated to the major data proteomics data resources. 
  • Submission to a public repository is recommended, if not mandated, by many of the major proteomics journals as part of the publication of a paper.
  • ProteomeXchange ensures that published (archival), raw and reprocessed (secondary) data is submitted and appropriately cross-linked. 
  • There are two pipelines for submission of MS/MS data, one for complete submissions (containing PRIDE XML) and one for partial submissions (containing raw data but no PRIDE XML). The ProteomeXchange submission tool is used for both routes.
  • PASSEL is the initial submission point of SRM data.
  • The submission process requires that you submit all available metadata, protein/peptide identifications and mass spectrometer output files for a rich dataset. Other data types can be submitted optionally.