Technical Overview, peak details.pl

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Revision as of 22:17, 15 May 2009

This script displays detailed information regarding other peptides that have signals close to the mass-to-charge readings of the peptide in question.

The arguments are pepid, pattern, delta_m, delta_f, and sort_type. pepid is the internal unique identifier for the spectrum associated with this specific peptide in the MRM library. pattern and sort_type are both used to generate links to other GPM resources. delta_m is the mass error range allowable for the parent ion. delta_f is the mass error allowed for any fragment ion.

Display Elements

• An overview of the base peptide:
  • The residue sequence.
  • The mass-to-charge ratio for the base peptide, and the parent ion mass error used in the calculations for signal uniqueness.
  • The charge state of the base peptide.
  • The calculated retention time for the peptide.
  • The accession number of the protein with which this peptide is associated.
  • The fragment mass error used in the calculations of signal uniqueness.
• A table containing the details regarding signal uniqueness.
  • The first column is a compound field containing the m/z ratio and intensity as recorded in the MRM database.
  • The second column is a compound field containing information for peptides which will generate signals close to the signal of the base peptide. If no signals were found in the data, the phrase No interfering signals will be printed. Otherwise, a table will be printed listing the details of the interference:
    • m/z @ I: the m/z ratio and intensity of the interfering signal
    • Peptides: peptides which will generate a signal at that m/z ratio.
    • Ret δ: difference from the base peptide of calculated retention time.
    • Proteins: a list of proteins in which this peptide is found.
  • If the m/z ratio of the interfering peptide is within the fragment ion mass error, but outside the calculated retention time window, the table will be printed with a light green background to indicate that this may be a usable signal for protein detection.
  • Tables printed with a white background have signals both within both the fragment ion mass error and retention time window, making the associated m/z peaks poor candidates for identification.