Protein Modifications

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Proteomics Standards Initiative


Protein Modifications



Group Chapter

Table of Contents

  1. Introduction
  2. How to comment
  3. Available data
  4. Tools
  5. Further information and relevant links


The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. For detailed information on all PSI activities, please see the home page. The protein modification workgroup focuses on developing a concensus nomenclature and provide an ontology reconciling in a hierarchical representation the complementary descriptions of residue modifications.

How to comment

If you would like to comment on the PSI-MOD document or , please submit an issue at:

The latest list of features to discuss/include in the future can also be found here:


Available data

The protein modification ontology (PSI-MOD) is available at the PSI-MOD GitHub site as an OBO format file.
A spreadsheet containing the mapping of the descriptive labels used in various databases and search engines, the concensus list of proposed short name for protein modifications established by collaborative effort of mass spectrometry community, and the proposed rules and recommendations for this nomenclature are available here. These short names are included in the ontology as synonyms of the corresponding terms.


  • PSI-MOD ontology can be searched by mass range: here
  • PSI-MOD ontology can be searched by tree browser: here
  • PSI-MOD ontology can be searched by term search: here


Further information and relevant links


Databases involved:

Companies involved: