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Digitizer Automatic Processing
This is the default mode for converting mass spectral images to mass - intensity lists. There are three methods available with Method 2 selected by default. That choice will usually work best, but images differ in their quality and those aspects can affect the results. So if you obtain poor results with Method 2, you can reselect the Automatic button and click Reset on the Setup window which will clear the mass intensity list but retain all calibration data, and then try Method 1 or Method 3. Different approaches can be tried repeatedly in this manner if necessary, but that should not often occur. There are also adjustment parameter boxes adjacent to the option boxes for Methods 2 and 3 that can be altered and which might improve results in some cases. Normally, those values will work best at their default settings of 90 and 10, respectively.
Automated processing will usually require additional post-processing for the best results. If a significant ion was missed, simply click on it at its top to add it to the list. Additional "phantom" ions may be identified in some cases, usually when the ion label is very close to the ion itself. Those can be removed by opening the Results table and double-clicking on the invalid mass value. Click OK to remove the value from the list.
Clicking Clear All will clear all the data, the calibration and the clear the current image, returning to the default startup condition.
In all cases, when an Autoprocessing is completed, the Manual mode will be set and you can select individual peaks to add by clicking on them. See Digitizer Manual Processing and Digitizer Options for additional information.