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The GPM can now be used to find proteins with specific modifications. While a shortcut for phosphorylation has been added to protein detail pages for human, mouse, zebrafish and yeast, this can be used with any protein accession number and modification mass.
The page, dblist_pep_modmass.pl requires both a protein accession number (e.g., ENSP00000343690, YGR254W) and a modification weight (79.96, 16). Example output can be seen here for accession ENSP00000343690 and here for accession YGR254W. The mass range of the modification is defined by the number of significant figures supplied with the modification mass as follows:
Optionally, the modification mass may be suffixed with an at symbol (@) followed by at least one letter denoting a residue. If residues are listed in this manner, the search will only return peptides which have a modification of the requested mass on at least one of the supplied residues. For example, a search for a modification of +15.997 on methionine only would be written 15.997@M, and the same modification for either methionine or tryptophan would be written 15.997@MW.
The data returned by the search is by peptide sequence, ordered by the start position of the peptide within the protein. The columns returned are:
The peptide sequence may be followed by the text "(N more)". This means that more than one identification of this peptide sequence has been identified for this protein with the requested modification. Clicking on the text will display the other peptide details, sorted by decreasing log(e) score.
Please read Mutated Protein Search.