The Tool Buttons - Crosslink Heatmaps
The Cross-link heatmap tool windows is another way of displaying your cross-links, once a search has finished.

Select two protein entries to be displayed from the protein lists (A). The reactive residues are then listed across the
horizontal and vertical axes on the heatmap (B). The entries can be the same protein twice for mapping intra protein
cross-links, or two different proteins for mapping inter protein crosslinks.
The heatmap then plots the number of cross-link observations that have scores above the score cutoff.

In the example below, we have searched a dataset from cross-linked calreticulin. We have then selected Calreticulin for
both the horizontal and vertical axis.

We have set the score cutoff to 20 (C), so that only results with scores of 20+ are plotted into the heatmap.
The cells are colored pink when there are few (1-5) observations, light red for 6-15 observations and dark red for 15+


Click any cell to list the scans in which the selected
cross-link has been observed. The colour of the
active cell then switches to grey.

In the example, we have clicked on the crosslink
between residues K64 X K153. The cell has a value
of 16, signifying that we have 16 observations with
scores above 20.

Click any entry on the result list to display the
annotated scan.
If you specified conditions when selecting your datasets, you can layout your heatmap by conditions, and the individual
results will be sorted according to the conditions.  In the example below, we have cross-linked a protein sample under two
conditions: with or without EDTA. At the same time, we have used two different cross-linkers (BS3-d0 and BS3-d4).

We type in the conditions when selecting the files
The heatmap by conditions distributes the observations according to condition and cross-linker.
When a cross-link has been observed with BOTH cross-linkers, the cumulated number of observations is written in a
separate column, in brown colour.