Tutorial
 
 
DOUBLECROSSED
When we think of cross-linked peptides, we traditionally think of them as something that occurs pairwise:
"peptide A has crosslinked to peptide B".

But be a little generous when pouring in your cross-linking reagent, and you will find that your protein forms so many cross-links that you can
easily have more that two peptides in the same precursor, following digest.

MassAI now comes with an optional feature, which identifies double cross-links.  This is obviously time consuming if you carry out a free-for-
all cross-link search, but you can cut down significantly on the search time by ticking the checkbox "Cross-link peptide ONLY if peptide has
been observed" (see below).
 
Here is an example of a tri-peptide intra-protein cross-link observed in Calnexin, using the standard BS3 crosslinking reagent.
The annotated scan shows fragment ions from all three peptides, along with a BS3 reporter ion, internal fragment ions and, in this case, the C peptide fragmented right after the BS3.

If a scan like this becomes too crowded, you can always toggle the individual peak groups on and off to get a clearer overview.