While Chromeleon processing methods include some default settings for working with MS data, these might not always be suitable for high-resolution MS data.
In general, you must review the settings on the MS Settings page and MS Detection page of the Processing Method to adjust to your data. Consider the following points:
- You can decrease the mass tolerance. In MS Settings > MS Chromatogram Settings, select the option to Manually define mass tolerance, and decrease it from the default 500 mmu to, for example, 6.0 ppm, that you also used during peptide mapping.
- You can select Inhibit integration for TIC channel to decrease the processing times during data analysis.
- Consider whether you want to apply smoothing or spectra bunching. Refer to the Chromeleon CDS Software User Help for details related to these settings.
- You can change the detection algorithm in the MS Detection page. Cobra, Genesis, ICIS, or Atlas are available and Genesis and ICIS are the most commonly used. For details about an algorithm, refer to the Chromeleon CDS Software User Help or to the dedicated section of the Ardia Data Viewer Application User Guide.