The Single Proteoform search node allows you to search your data for a single user-defined proteoform without having to create a database. The user-defined proteoform is input in the ProForma format, which consists of the backbone residues in single letter amino acid abbreviation and modifications entered in brackets after the residue which is modified. The modifications can be entered in the following ways:
- a PSI-MOD number
- a RESID ID number
- a UNIMOD accession number
Each of the sources (PSI,RESID, and UNIMOD) are databases of known protein modifications. Modifications are linked to an ID or reference number. These numbers are used in the Single Proteoform search to represent the modification.
When entering a modification use the following syntax:
Database | Example |
---|---|
PSI MOD | MOD:00057 For example: …SGRG[MOD:00057]K… |
UNIMOD | UNIMOD:1 For example: …SGRG[UNIMOD:1]K… |
RESID | RESID:AA0048 For example: …SGRG[RESID:AA0048]K… |
For a full list of modifications, visit the following websites:
- UNIMOD (https://unimod.org)
- RESID (https://proteininformationresource.org/cgi-bin/resid.pl)
- PSI-MOD (https://www.ebi.ac.uk/ols/ontologies/mod)