Following a search, you can bring up the "Theoretical Peptides" window, by pressing the "T.pep" button in the tool-button window.
Press "List peptides" in order to populate the table with all theoretical peptides in your search space.
(It is left unpopulated at start, as the number of theoretical peptides may grow too large to be of any use when you work with a
The peptides are listed along with information on how many times it was observed during the search, mass, cross-linkability,
missed cleavages ...and more.
Below is the output from searching a dataset from a cross-linked sample (BS2G-d0 and BS2G-d6).
The table has been sorted by the number of observations, in descending order. Notice that almost all the top scoring peptides are
modified with a "dead-end" cross-linker, suggesting that the sample has been oversaturated with cross-linker.
Trypsin is not able to cleave a LYS if it has been modified with crosslinker, and this reflects on the missed-cleavages histogram. We
can see, that the most commonly observed peptides have 2 missed cleavages