Metadata requirements for MS/MS submissions

Proteomics data is substantially enriched when it is accompanied by sufficient metadata. The repositories in PX are quite flexible about how much experimental metadata they will accept. Below we summarise what you must supply when submitting your data to PX. We recommend that you add extensive metadata in the interest of making your dataset as useful as possible in the future.

The following details are mandatory for any PX submission:

  • Contact details - name, e-mail and/or institution of one person responsible for the submission; this enables future users of the data to contact the original authors
  • Title of the PX dataset
  • An abstract describing the dataset
  • A list of keywords - comma-separated
  • Literature references associated with the data. In some cases there may not be an associated reference as you will need to submit your data before its associated manuscript can be submitted.


This table lists metadata we recommend that you supply from each mass spectrometer run for complete submissions as well as partial submissions as this will ensure a more informative dataset:

Metadata Complete Submissions Partial Submissions
A short-label for the experiment - describing the experimental factor (technical or biological replicates)  Yes  
Sample name - when there are many samples in an experiment  Yes  
Sample species - if this is added you will need to add at least one NEWT [3] term  Yes Yes 
Extra information about cell type/tissue - or other of information about the biological sample   Yes  
Protocol name - name for the experimental protocol - if this is added at least one 'protocol step' needs to be provided   Yes  
Instrument - Make and model of instrument, ionization source, analyser/s and detector. If this metadata is added  the fragmentation technique needs to be provided   Yes Yes
Processing software/search engine used   Yes  
Post-translational modifications (PTMs); these can be reported using the PSI-MOD ontology [4], a simplified version of it is provided through PRIDE Converter 2   Yes  Yes
Search database used to produce the search engine output files  Yes  Yes