GPMDB uses an evidence code system to rate the current observation status of individual protein sequences. The same system is used for gene loci, where applicable. The ratings are as follows:
| Code | Level | Meaning |
|---|---|---|
| black | 1 | no observation of a protein has reached a set scoring threshold |
| red | 2 | at least one observation of a protein has exceeded the scoring threshold |
| yellow | 3 | multiple observations of a protein have a set of common peptides and the distribution of scores for at least one peptide in that set exceeds a minimum test for non-randomness |
| green | 4 | the set of common peptides contains at least one peptide with a scoring distribution that exceeds a stricter test for non-randomness |
The method for calculating these evidence codes in Perl can be found in the subroutine "gpmdbProteinModel" in gpmdb_rest.pl.