In the sheet for the results of composite scoring, consider including the following information:

  • An area where you use individual report variables from the procMeth.compScoring category to report the values of the parameters that were used for composite scoring. For example:
    • To report the mass accuracy threshold, use report variables massAccuracyThreshold and massAccuracyUnit.
    • To report whether intensity threshold was used to exclude low-abundance isotopes, use filterIsotopes.
  • A table for the composite scoring results. Start with the table from the MS tab of the Integration table from the Results group of templates. Keep the retention time column and edit the remaining columns to report the following:
    • To report the overall score, use report variable peak.compScoring.score("ProcessingMethod").
    • To indicate whether peaks were excluded, use the values of report variable peak.confirmationPeak(n).isExcluded with n from 1 to 4.
  • A table for the isotopic dot product results. Start with a copy of the composite scoring results table and edit the columns to report the following:
    • The value of peak.compScoring.isoDotProduct.
    • Whether the value meets the threshold.
  • A table for the mass accuracy results. Start with a copy of the composite scoring results table and edit the columns to report the following:
    • The values of peptide.massAccuracy(n) with n from 1 to 4.
    • Whether all four values meet the threshold.
  • TIP

    Remember that the massAccuracy variable might return text like “Peak is excluded per composite scoring filtering criteria”.

  • A table for peak apex alignment results. Start with a copy of the composite scoring results table and edit the columns to report the following:
    • The value of peptide.peakApexStdDevWithinChargeState.
    • Whether the value meets the threshold.

TIP

To filter the tables so that they display rows only for charge states, use the Filter Peaks page of the Properties dialog. Filter the table based on component names. Names of charge states begin with “(+”.