Technical Overview, peptide xlib.pl

This script will illustrate the effects of differences in peptides (modifications, mutations or residue gain/loss) on the spectrum for that peptide.

The required arguments are proex, fe_type, fe, mods, mass, id, seq, uid, int_values, path, ltype, end, mass_values, homolog, label, z and start. proex, path, ltype and homolog are used to construct links to other GPM resources. fe_type and fe are the measurement unit type (either Daltons or ppm) and measurement error, respectively. mods is a formatted list of modifications to the peptide being displayed in the format mod_mass:prompt_loss@X[residue_number], with X as the residue being modified. id is not currently used, but reserved. seq is the residue sequence. uid is the identifier in the original data file for the spectrum used to identify this peptide. int_values is a list of intensities for the m/z list, in order. start and end are used to position individual residues within the peptide. mass_values is the list of m/z values for this peptide. label is the accession number of the protein to which this peptide observation applies. z is the charge state of this peptide as measured by the instrument that generated the original data file.

Display Elements

• A form for redisplaying your proposed changes:
  • The residue sequence currently being inspected.
  • The error range in the measurements.
  • A list of modifications to consider when drawing the spectrum, formatted as explained directly beneath it.
• A calculated spectrum for the peptide described in the form above, showing the m/z and intensities of the peaks and an error measurement per peak.
• A table of all possible fragmentations of the peptide being inspected, colour coded to show which of the theoretical peaks are matched by the measurements recorded by the instrument that generated the original data file.