Mutated Protein Search

Revision as of 15:08, 4 February 2014

Description

The GPM can be used to find instances of proteins with Single Amino acid Variants (SAVs).

Examples

The page, dblist_protein_mut.pl requires a protein accession number (e.g., ENSP00000343690, YGR254W) as input. Example output can be seen here for accession ENSP00000343690 and here for accession YGR254W.

Data

The data returned by the search is ordered by the location of the mutation. 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. SAV: A listing of the original residue, its position in the protein and the resulting residue in HGVS notation as well as the reference accession number of the variant, when available.
7. peptide: A clickable link showing the peptide sequences associated with this protein. Clicking the link will open the peptide details page for that 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 observation of this peptide sequence has been identified with a specific mutation. Clicking on the text will display the other peptide details, sorted by worsening log(e) score.

Finding Modifications

Please read Modified Protein Search.