Proteomics Guidelines

This guide refers to SEEK, but is also relevant for FAIRDOMHUB, which is an instance of SEEK.

The MIAPE standard (Minimum Information About a Proteomics Experiment) follows the same principles as the longer established MIAME standard for transcriptomics. It is a set of guidelines describing the minimum information required to adequately record a proteomics experiment (i.e. where the samples came from, how they were analysed and what equipment was used etc) to allow others to understand and potentially reuse data.

There is growing interest in the MIAPE standard from publishers, and some journals now require MAIPE compliant data in order to publish. This is not yet as widespread as the requirement for MIAME compliance in transcriptomics, but it is still increasing.

For SEEK, we recommend you adopt a MIAPE compliant data template where possible.

Proteomics experiments vary widely and cover many different techniques. MIAPE is therefore a collection of reporting guidelines for the different technologies available. Examples include:

  • Reporting guidelines for molecular interaction experiments (MIMIx)
  • Reporting guidelines for Mass Spectrometry experiments
  • Reporting guidelines for Mass Spectrometry Informatics experiments
  • Reporting guidelines for Gel Electrophoresis experiments
  • Reporting guidelines for Column Chromatography
  • Reporting guidelines for Capillary Electrophoresis
  • Reporting guidelines for gel image informatics (under development)

The associated examples are templates for Mass Spectrometry experiments. These have been developed by the Pride PRoteomics IDEntifications database and more details can be found on their website

Embedded in the spreadsheet are some macros that will help you annotate your data with terms from controlled vocabularies where appropriate.


SEEK documentation is a community driven activity. If you have any modifications you want to make to the guidelines please send requests, or feedback to