To adjust the parameters of the processing method that relate to components, open the MS Component Table in the Processing Method pane. Consider the following points:
- You can allow for wider RT windows. The RT windows that are calculated automatically during the import of a target peptide list are usually very narrow. You can change the RT window values in the Window column. Similarly, you can widen the Display Window value from RW (retention window) to 2.0, for example.
- If peaks are split, you can apply smoothing. You can apply smoothing globally, from the MS Settings page; see Setting up the processing method. Alternatively, you can apply smoothing to XICs only. This is done in the same dialog box as Updating XIC filters for all components.
- The peaks might appear split when an XIC contains data points from both the full-MS and MS2 scans. To apply a filter that considers only the full-MS data, see Updating XIC filters for all components.