Technical Overview,

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This script displays the spectra in order of identification from a GPM result file, along with other identification information.

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

Display Elements

  • a list of links to other scripts on the GPM.
  • a form to view peptides with specific modifications or mutations.
  • a table of peptide information:
    • Spectrum: the spectrum identifier in the original data file.
    • log(e): the expect score; the base-10 logarithm of the probability that this peptide identification was a random match.
    • log(I): the base-10 logarithm of the sum of the intensities of the raw intensities of the signals for this spectrum.
    • m+h: the mass of the peptide, in Daltons.
    • delta: the difference between the measured and theoretical mass of the peptide.
    • z: the charge of the peptide.
    • retention: the retention time, as measured by the instrument that generated the original data file submitted to the search software on the GPM.
    • sequence: the amino acid sequence of the peptide. The number in parentheses is an AJAX-generated count of the number of identifications for this peptide in the GPMDB.
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