The Tool Buttons - Viewing the scan
The annotated scan is displayed automatically, whenever a result is selected from one of the result tables.
If you close this window for any purpose, you can always open it again by pressing the "SPEC" button in the tool-button

MassAI annotates a variety of different fragment ions, including b,y,c and z ions, neutral losses, oxonium ions and
internal fragments. The individual groups of fragment ions can be turned on/off by using the checkboxes in the lower part
of the window.
When you have a particularly crowded scan, visually separating the different types of peak can be helpful in recognising mass-
related patterns between peaks. 
Select 3D view to see the scan in a parallax 3D perspective. b,y,c,z ions are in the front row, neutral losses and internal fragment
follow behind, and un-annotated peaks are moved to the rear. The scan is rotatable around the 3 XYZ axis.
Another way of isolating relevant information in a scan is to separate the different groups of ions into individual sub-scans. This is
done by setting the "Split into subscans" checkmark.
This generates a set of new subscans, which contains the isolated fragment ions, neutral losses and glycan fragments. In case of a
cross-link, fragment ions from each peptide is shown in separate sub-scan.
Subscan displaying only the recognised fragment ions of a peptide
Subscan displaying only the recognised neutral losses from same peptide
Two subscans, each displaying the fragment ions of one peptide in a cross-link
Peaks stemming from internal fragmentation of a peptide are rarely used for the actual identification of a peptide. However, they are useful for
validating the proposed peptide. This is especially useful when working with cross-linking, where the "B" peptide generally fragments more poorly
than the "A" peptide. It is common to observe peaks from internal fragmentation, which contain the actual cross-linked residues along with parts of 
either peptide.
Annotated scan, displaying only ions from internal fragmentation of the peptide