The Tool Buttons - Glyco Profiling
When you include glycosylations into your search criteria, recognised glycopeotides are listed in a separate table in the result output
window. Just like any other type of result, you can select any entry in order to bring up the annotated scan.
Glycosylation is a heterogenous type of modification. For the N-linked type, each modified residue can carry a variety of
glycosylations, all of which may be present simultaneously in the same sample. Therefore we are often interested in characterising the
entire glyco profile for each residue rather thn simly looking through each result one by one.
This is where the "Glyco Profiling" feature comes in handy.
A
B
C
D
E
F
G
Table A lists the proteins in which glycopeptides have been observed.
Selecting one of the listed proteins populates table B with a list of the glycosylated residues for selected protein.

Selecting an entry in table B carries out two things:
1: Table C is populated with the individual glycopeptide observations for this residue, along with the name of the glycosylation, the
score and scan number. Selecting any of these brings up the annotated scan, just af if you had selected the same result from the scan
result window. If your dataset is large, you will most likely have many observations of the same type of glycan (e.g. mannose 9).

2: The pie chart E is populated with the same information as in table C, only in a graphical manner, where you can see the
distribution between the different types of glycan on the selected residue. We can see from the rightmost table in window E that
residue 616 is populated with high-mannose structures ranging from 9 to 13 mannoses, some of which carry phosphorylations. (It is a
yeast sample, hence the large sugar structures). Select any group of glycosylation in this table to populate chart G with a graphical
overview of the scores of each observation for this glycan. In the above example, we have 10 observations of a mannose 9 on residue
616.
Chart G shows that 9 out of these are in the high scoring range above 50, one has a score just above the cutoff (making  total of 10
observations). (Use the sliders in panel F to set the score cutoff). An additional two observations are shown in dull red. these have
scores below the cutoff , and are not included in the 10 observations. You can change the cutoff at any time, and the colouring in chart
G will reflect the changes accordingly.
In the above example, we have shown a simplified view, where there is only one pie chart present.
MassAI however, shows two pie charts per default, each of which can be assigned to one file in the dataset at a time. This can be
used to pinpoint differences in the glycoprofile between two experimental setups.

Drag the vertical bar between the charts to change the size of the individual pie charts.