Typically, your report templates include abundance calculations of specific peptide modifications and indicate whether these levels pass the quality criteria that are defined for your peptide. These calculations are based on the areas (or heights) of peaks corresponding to the modified and native peptides.

Procedure

  1. On a new report page, insert the Summary table found in the Peak Summary Table template inside the Results group of table templates.
  2. Open the Properties dialog for the table.
  3. On the Filter Injections page, select the types of injections whose data you want to include in the table.
  4. Edit the retention time column by selecting the MS Quantitation channel and the component that corresponds to the oxidized peptide.
  5. Report the peak area for the component that corresponds to the oxidized peptide as follows:
  6. Edit the column that reports the peak area (of any channel and component selected in the navigation pane).
  7. Change the report variable from peak.area to injection.chm("MS Quantitation", "oxidized peptide component name").peak("by name", "oxidized peptide component name").area
  8. In another column, repeat the previous step to report the peak area for the component that corresponds to the native peptide as injection.chm("MS Quantitation", "native peptide component name").peak("by name", "native peptide component name").area

  9. NOTE

    In some cases, you might need to modify the formulas to sum peak areas of several components, for example, if an oxidation includes several isomers of a peptide.

  10. In yet another column, divide the peak area of the oxidized peptide by the sum of the peak areas of the oxidized and native peptides, and format the value as percentage.
  11. This column now reports percentage of oxidation for the peptide across injections in the sequence.

  12. TIP

    • To visualize the results of your calculation, use a report chart that displays the percentage of oxidation across injections of the sequence.
    • In the cases when several different components contribute to a modification, you might want to calculate and plot the percentage of modification for each contributing individually.
  13. In the last column of the table, evaluate whether the calculated modification abundance passes or fails the criteria, either by using the if() formula or by using conditional formatting.
  14. After you have defined the table and a chart for one peptide oxidation, you can copy, paste, and edit the copy so that it reports data for another oxidation.
  15. Similarly, you can copy the entire report template sheet, and use the copy for calculating and reporting other kinds of peptide modifications, like deamidation, N-glycans, and so on.

NOTE

  • In the case of deamidation, remember that two modifications contribute to the percentage of deamidation, that is, the peak of the succinimide intermediate and the peak of the isomeric acid.
  • In the case of N-glycans, remember to account for all the possible N-glycans.