Modified Protein Search

Latest revision as of 22:10, 7 April 2011

Description

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.

Examples

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:

δ(modification weight) = (0.5 / 10ⁿ)

where

n = the number of significant figures in the Mod mass field.

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.

Data

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:

1. #: The row number of results (twenty unique peptides are displayed per page)
2. log(e): The base-10 logarithm of the odds of a false positive identification.
3. m+h: The mass of the peptide in Daltons.
4. delta: The difference between the measured mass and the theoretically derived mass of the peptide.
5. z: The measured charge of the ion.
6. Mod pos: a list of the positions in the protein which contain the requested modification. If you have defined specific residues in your search, the list will contain only the positions that match your requested residues.
7. peptide: A clickable link showing the peptide sequence which contains your requested modification. Clicking the link will open the peptide details page for this specific identification. Also included is the number of identifications of this peptide in GPMDB.

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.

Finding Mutations

Please read Mutated Protein Search.