The coverage view is a central piece in our final delivered report. It provides an intuitive way to visualize the degree of confidence the experiments and analyses will deliver. We created this example so that you can see it yourselves.
How to read the coverage view?
The region annotation legends illustrate the meaning of the colours used in the region row in the view, with green and orange representing the framework and the CDR of the variable region respectively, and dark blue representing the constant region.
The sequence coverage legend shows the relation between the colours of bars in the coverage view and the source where the data come from. You can turn on and off some of the bars by select or deselect the checkbox to the left hand side of the legend. Right now, you may see peptides spectrum matches from samples digested by six different enzymes: Trypsin, Chymotrypsin, AspN, Pepsin, GluC, ProteinaseK.
The modification highlight includes all the post translational modifications (PTMs) observed in the select samples. They are ordered by the number of occurrences (the frequency) in the list, in descending order.
In the body of the coverage view, the region annotation and the peptide spectrum matches (PSMs) are displayed above and below the antibody protein light chain sequence respectively. The PSMs are displayed as coloured bars. The dots on the bars represent the PTMs. If a PTM is selected in the modification highlight list, the dots representing that particular PTM will be highlighted and other PTMs will be faded. If you point the mouse cursor on a PSM, a tooltip will be displayed with information such as the position of the peptide in the protein, the enzyme used to digest the sample, the scan number, the retention time, the precursor m/z and charge, the intensity of the peak area (the MS1 feature) and the peptide sequence.
While the many PSMs displayed on the coverage view show high confidence, it is sometime hard to visually see the alignment between the sequence and the bars especially when the PSMs are further down away from the sequence. To facilitate a better visual alignment, you can click on the amino acid in the antibody protein sequence. This will create a vertical ruler surround that position. Click the same amino acid again to hide the ruler.