Check Differences Tool
The interpretation of mass spectra typically involves a seemingly never-ending check of the differences between all peaks in a spectrum (e.g. de novo peptide sequencing, characterization of post-translational modifications). The Check Differences module [Tools → Check Differences] is able to simply generate a table of all the differences between the peaks in a peaklist. This table can then be used to automatically compare, within a specified tolerance, each difference with the respective masses of all amino acids, calculated dipeptides, and pre-defined modifications, as well as with a specified mass value or molecular formula.

Check differences tool.
Tolerance settings
To set Tolerance use [Config → Tolerance…] . In the dialog you can specify the value and units (Da, ppm, %). Current tolerance settings is always shown in the application statusbar.

Tolerance dialog.
Mass type settings
It is important to set proper mass type for masses calculations - Monoisotopic Mass [Config → Monoisotopic Mass] or Average Mass [Config → Average Mass]
. Current mass type is shown in application statusbar.
Generate table
To generate the table of differences press Generate button located in module control panel. All matched differences will be highlighted. To see the difference details click to appropriate difference and check the control panel.
Check for specified value
Beside the list of aminoacids, dipeptides and modifications you can also search for specified mass shift. In the Difference field you can specify the difference or you can use simple molecular formula (gain-loss, e.g. Na-H).
Mass limit
To speed-up the table generation, Mass limit can be set in control panel to skip calculation of higher differences.