The Protein Coverage table displays peptide sequences and corresponding protein coverage. The accompanying display maps the protein sequences of detected peptides to colored lines below each sequence representing colors assigned to different MS samples:
The Protein Coverage table also includes the following specialized menu icon buttons:
• The gear icon opens the Protein coverage rendering options dialog:
Show fragment coverage: b/y cleavage info are displayed in blue and red, respectively, in the Protein Coverage window:
Show Protein highlights on missing fragments: where b/y ions are missing is highlighted in yellow:
It's worth noting that the peptide terminals are considered as "fragments" in addition to any MS2 ions. ie. even if there are no b/y ions, if there is a peptide terminus, that is supporting data for the peptide bond, and hence a blue and red marks are shown at that site.
In the report tab, fragment coverage information can be displayed in the Summary tab; Edit > Current tab settings > Edit summary template > Short codes > [FragmentProteinCoverageImage]