Technical Overview, dblist pep modmass.pl

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Revision as of 23:12, 18 February 2009

This searches GPMDB for instances of peptides from a specific protein that contain given modification. This differs from the action of dblist_protein_mod.pl which searches for proteins with known SNAPS, not mutations.

The two required arguments are label and modmass. The label argument is a protein accession number for the protein in which you wish to locate modifications. The modmass argument is a mass modification (positive or negative), followed by an "at" symbol (@), followed by the residues on which the modification may be located. E.g, phosphorylation can be searched for with a modmass argument of "80@STY".

The optional arguments are proex, offset and display. The proex argument is used in link creation to other pages in the GPM. The offset argument controls the first result to view, and defaults to zero to show the first result. The display argument is used control the appearance of the form at the top of the page; a value of 1 displays a form tailored to searching for phosphorylation, and a value of 0 displays a form where custom modifications may be entered.

Display Elements

• the human-readable detains regarding the protein accession number, offset with a highlighted background.
• navigation links to page through the results of the search, twenty results per page.
• the search results:
  • #: the result number.
  • log(e): the expect value. This is the base-10 logarithm of the chances of this peptide identification was an accidental, random assignment. E.g., if the expect value is -4.0, the odds of this identification being erroneous is 1 in 10,000.
  • m+h: the mass of the peptide, in Daltons.
  • delta: the difference between the mass as measured by the instrument that generated the data file that was submitted to the GPM's search software and the theoretically calculated mass of the peptide based on the residue sequence.
  • z: the charge of the peptide, as measured by the instrument that generated the data file that was submitted to the GPM's search software.
  • Mod pos: the 1-based location of the modifications in the protein sequence. If a peptide contains more than one modification, the positions will be listed in ascending order.
  • peptide: a compound field.
    • The first element is the peptide sequence, bracketed by up to four residues of context from the full protein sequence.
    • The second element appears when there is more than one peptide identification for this protein with the same SNAP. If there is text that reads (X more), with X as a number, clicking this text will display the other peptides from this protein that have the same mutation at the same location.
    • The third element is a number in parentheses, e.g. "(85)", which denotes the number of identification of this peptide sequence across all peptides in GPMDB. This number is one piece of AJAX-generated content that appears on result, protein and peptide displays in the GPM.

This script uses the following tables: in EnspMapDB, map. In GPMDB, paths, result, protein, peptide, proseq, aa.