Spectra Processing

General information

The purpose of this module is quick automated spectra processing with a defined set of modules and parameters. This is similar to the batch mode for peak lists. The modules and their parameters can be configured by opening a scan and pressing the "Spectra processing" button. Please note, that the aim of this functions is not to identify compounds by looking at a single spectra. The target is to give the user a quick overview over a specific scan.

Processing queue

The processing queue is, if enabled, automatically executed sequentially from top to bottom. Most modules require a mass detection to be run first.

Adding modules & Setting parameters

Modules can be added to the processing queue by double-clicking or pressing the "Add" button. Modules can be removed from the processing queue by pressing the "Remove" button. The parameters can be set using the "Set parameters" button or by double-clicking on a module in the processing queue.

Displaying results

Every module has the parameters "Display results" and "Dataset color". "Display results" specifies if the results of a module should be displayed in the plot or just be passed to the next module. The results of the last module in the processing queue will be displayed regardless. "Dataset color" specifies a color, the results should be displayed with in the spectra plot.

Troubleshooting
Nothing is happening, even though the processing is enabled.
Check the parameters or the modules. For example, if the mass detection is set to a specific noise level for one MS1 scan and the intensities vary between scans, the noise level might be too high. If switching between MS1 and MS2 scans, this is especially relevant.