The protein inference graphs makes it easier to understand the complexity of protein inference and evaluate the evidence for the individual proteins.
There are three main versions of the protein inference graphs:
Lines: A line between a peptide and a protein is drawn if the sequence of the given peptide can be found in the
protein. A fully drawn line means that the peptide sequence is enzymatic in the protein, i.e., adhering to the cleavage rules of the
enzyme used, while a dotted line represents a non-enzymatic peptide sequence.
Selection: By default the protein(s) if the currently selected group and its corresponding
peptides are selected. Click a peptide or protein to select it and its nearest neighbors. To only show unique neighbors
select the "Unique Only" option at the bottom. To visually indicate the selected peptides and proteins select the
"Highlight" option. A list of all the currently selected peptides and proteins is shown by clicking the peptide and
protein counts in the upper right corner.
To select more than one peptide or protein, or to deselect a peptide or protein,
hold down the "Shift" key when clicking the wanted peptide or protein. Clicking in an empty area of the graph will remove all
selections, while "Ctrl+A" can be used to select all peptides and proteins.
The currently selected peptides and proteins can be listed by clicking the links in the upper right corner.
Layout: Click and hold to move the currently selected peptides and proteins. The layout can always be reset by clicking the
"Layout" option in the upper left corner.
Export: The protein inference graph can be exported to an image file via the "Export" option at the top.