| Line 8: | Line 8: | ||
:::ACCESSION:pm.Xnn+MODIFICATION | :::ACCESSION:pm.Xnn+MODIFICATION | ||
| - | where "ACCESSION" is the accession number for the protein, " | + | where "ACCESSION" is the accession number for the protein, "pm." indicates that it is a protein modification, "X" is the single letter symbol for the amino acid residue, "nn" is its ordinal position in the protein, "+MODIFICATION" specifies the change. For example, using the PSI-MS annotation for modifications, the notation |
| - | :::ENSP00000339186: | + | :::ENSP00000339186:pm.T262+Phospho |
indicates that for the protein accession number ENSP00000339186, the threonine residue number 262 is phosphorylated. It should be noted that the "+" symbol indicates that the side chain has changed: the change may result in either an increase or decrease in residue molecular mass. | indicates that for the protein accession number ENSP00000339186, the threonine residue number 262 is phosphorylated. It should be noted that the "+" symbol indicates that the side chain has changed: the change may result in either an increase or decrease in residue molecular mass. | ||
| Line 22: | Line 22: | ||
where "=NEW_RESIDUE" uses the residue-specification ontology required. Using this strategy for naming the modification in the previous example: | where "=NEW_RESIDUE" uses the residue-specification ontology required. Using this strategy for naming the modification in the previous example: | ||
| - | :::ENSP00000339186: | + | :::ENSP00000339186:pm.T262=MOD:00047 |
indicates that for protein accession number ENSP00000339186, the threonine resiude number 262 has been replaced with the residue specified by the PSI-MOD ID "MOD:00047" (O-phospho-L-threonine). | indicates that for protein accession number ENSP00000339186, the threonine resiude number 262 has been replaced with the residue specified by the PSI-MOD ID "MOD:00047" (O-phospho-L-threonine). | ||
Contents |
While there have been efforts to create ontologies and controlled vocabularies to describe the various types of amino acid modifications that can be observed in proteomics, there has been no proposed succinct notation for describing those modifications in their biological context. This document lays out such a notation, using a format similar to the Human Genome Variation Society's notation for describing protein amino acid polymorphisms.
The general nomenclature format proposed for the case where the modification is being described as a change to the structure of the amino acid residue in question:
where "ACCESSION" is the accession number for the protein, "pm." indicates that it is a protein modification, "X" is the single letter symbol for the amino acid residue, "nn" is its ordinal position in the protein, "+MODIFICATION" specifies the change. For example, using the PSI-MS annotation for modifications, the notation
indicates that for the protein accession number ENSP00000339186, the threonine residue number 262 is phosphorylated. It should be noted that the "+" symbol indicates that the side chain has changed: the change may result in either an increase or decrease in residue molecular mass.
Another approach taken to specifying residue modifications is to consider each modified residue to be a completely new amino acid: the PSI-MOD ontology uses this philosophy. If this type of residue replacement idea is useful for a particular type of study, then the notation used will be:
where "=NEW_RESIDUE" uses the residue-specification ontology required. Using this strategy for naming the modification in the previous example:
indicates that for protein accession number ENSP00000339186, the threonine resiude number 262 has been replaced with the residue specified by the PSI-MOD ID "MOD:00047" (O-phospho-L-threonine).