Figure 1

XLPM implements a unique filter based on high probability to observe a complimentary y-ion, given a b-ion. For each candidate pair of cross-linked peptides and for each possible cross-link position theoretical masses of b and y ions are computed. Next, the candidate experimental spectrum is checked for the presence of b-ions. In every case when charge of b-ion is less than the charge of the precursor, the experimental spectrum is searched for the complementary y-ion.