Technical Overview, peak search.pl

This script shows the result of searches done on the MRM data stored in the GPM. Searching can be done on any combination of parent ion mass, peptide sequence or accession number.

This script has two different displays; one for mass or sequence searching and one for accession numbers.

Display Elements - Mass or Peptide Sequence Search

• a search form, for refining results or beginning a new search.
• The table of results:
  • Sequence: the peptide sequence associated with the spectrum in the same row.
  • m/z: the mass to charge ratio.
  • z: the charge.
  • # Obs: the number of times this peptide has been identified in GPMDB.
  • Accession: the accession number of a protein in which this peptide was found.
  • Pos: the position of this peptide in the protein identified by the accession number on that row.
  • Data: a compound field with three elements:
    • The Spectrum button leads to peptide_xlib.pl for this spectrum.
    • The Details button leads to peak_details.pl, to give a more detailed explanation of the spectrum.
    • The + button shows or hides the spectrum table associated with this peptide. The top row is a list of m/z values, and the bottom row is the intensity corresponding to that m/z peak.

Display Elements - Accession Search

• a form to search for identifications of this protein in GPMDB using dblist_label.pl.
• descriptive text regarding the protein, highlighted in yellow.
• a form to change the view of this page between HTML and a spreadsheet-compatible form.
• the table of results:
  • Peptide Sequence: the residue sequence of the peptides identified in this protein.
  • Charge: a field of the charge states in which this peptide has been observed.
  • Ret: the calculated retention time of this peptide.
  • MRMs: the number of records in the MRM database for this peptide.
  • Observed z=1: the number of times this peptide has been identified in GPMDB with z=1.
  • Observed z=2: the number of times this peptide has been identified in GPMDB with z=2.
  • Observed z=3: the number of times this peptide has been identified in GPMDB with z=3.
  • log₁₀(ω/ω₀) z=1: the log of the normalized count of identifications of this peptide in GPMDB with z=1.
  • log₁₀(ω/ω₀) z=2: the log of the normalized count of identifications of this peptide in GPMDB with z=2.
  • log₁₀(ω/ω₀) z=3: the log of the normalized count of identifications of this peptide in GPMDB with z=3.