To set up composite scoring, follow these steps:
Procedure
- If not already displayed in the Processing Method pane, display the Composite Scoring page by doing one of the following:
- Use the Page Selector.
- Select a layout from the Layouts palette that includes the Composite Scoring page. For example, you can use the MS Quantitative layout.
- In the Criteria area, clear Confirming Ion Ratio Passed.
- This option is mainly for small molecules.
- Select all the remaining three options: Isotopic Dot Product, Mass Accuracy, and Peak Apex Alignment.
- For detailed explanation of these criteria, refer to the Chromeleon CDS Software User Help.
- Adjust the value for the Mass Accuracy to 6.0 ppm, which was also used during peptide mapping. Keep the other two criteria at their default values.
- At the top of the Composite Scoring page, set the number of criteria that must pass so that the component is scored as passed and the number of criteria below which the component is scored as failed. As the most stringent pass or fail criteria, set both values equal to 3.
- Composite scoring of the target peptides is now set up. When you select the MS Quantitation channel, all components in the navigation pane are marked with an icon indicating whether the component passed, passed with only some of the criteria, failed, or was not found.
NOTE
Only charge states of peptides are scored. Icons for a master peptide are linked to the results of the corresponding charge states.
IMPORTANT
If you have selected the MS Settings option to inhibit integration for TIC channel, all components are marked as not found when you select this channel in the navigation pane. Scoring only proceeds with the MS Quantitation channel.