- 1-PSI-MOD : a community standard for representation of protein modification data

Large-scale proteomics experiments are beginning to expand our understanding of protein function in cell physiology. However, integration of experimental data from proteomics research is hampered by fragmentation of publicly available data. Data on protein modification can be particularly difficult to interpret because of different nomenclatures in common use, and of different conceptual approaches, such as those adopted by RESID, UniMOD and DeltaMass, reference databases describing modifications of amino acids. As workers in proteomics, mass-spectrometry and bioinformatics, acting with others to develop and promote standards for storing data and submitting and publishing results, we propose a community standard ontology that reconciles complementary descriptions of residue modifications in a hierarchical representation, and provides a tool for precisely annotating ambiguous or incomplete experimental results. This ontology has been developed by a work group of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) and is available in OBO format at