Technical Overview,

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This script displays information about a single protein identification from a GPM result file.

The required arguments are path, proex, label, homolog, uid, npep and ltype. path is the file system path to the GPM result file. proex, uid, homolog and npep are used to create links to other scripts on GPMDB. ltype controls the appearance of display elements on the page.

Display Elements

  • a table of links to both GPM and external resources.
  • a form to control the display of both the AJAX-generated content and list of peptides used to identify this protein.
  • a coverage diagram of the peptides identified for this protein.
  • (validate): a link to
  • (mrm): a link to, if this protein is contained in the peakdb tables.
  • a colour-coded display of the residues in this protein sequence. Red residues are part of a peptide in the GPM file; green residues are areas of the protein unlikely to be covered by peptides due to either their length or hydrophobicity.
  • a table of peptide identifications for this protein:
    • spectrum: the identifier for the spectrum associated with this peptide.
    • log(e): the base-10 logarithm of the chances that the identification of this peptide is a random match. E.g., a log(e) score of -3.0 corresponds to a 1 in 1000 chance of a false positive identification.
    • log(I): the base-10 logarithm of the raw intensities associated with this spectrum.
    • m+h: the weight of this peptide, in Daltons.
    • delta: the difference between the measured mass and theoretical mass of this peptide.
    • z: the charge of the peptide, as measured by the instrument used to generate the data file given to the search software on the GPM.
    • sequence: the residue sequence of the peptide. Residues highlighted in blue are modified proteins. Residues highlighted in red are mutations.
    • n or ω: AJAX-generated content about this peptide. n corresponds to the count of identifications of this peptide in the GPMDB. ω corresponds to the relative frequency of identification of this peptide for this protein in this GPM result file.
  • Protein Information: information about this protein from external sources (e.g., ENSEMBL or IPI), cached on the GPM.
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