Fig. 4.

Results from the analysis of the CRM complex and BSA data sets. A, Numbers of identified URPs in the CRM data set. Identified URPs that link residues covered by the PDB structure 3GJX were analyzed by TopoLink. The red bars are the proportion of URPs linking residues that are either not solvent accessible, or are farther away than 35 Å according to the SAS distance. The green bars are the proportion of URPs that were not covered by the structure. OpenPepXL identified 78 URPs. 44 URPs were validated and one link is inconsistent with the structure (IWS) with a distance of 37.4 Å between linked residues. Kojak identified 61 URPs of which 41 were validated. pLink2 identified 78 URPs of which 38 were validated and two are IWS, including the same 37.4 Å link as OpenPepXL and an additional IWS link with a 40.4 Å distance. StavroX identified 48 URPs of which 28 were validated and one is IWS. XiSearch found 36 URPs of which 24 were validated and xQuest found 16 of which 14 were validated. B, Numbers of identified URPs in the BSA data set. OpenPepXL and xQuest were compared on ion trap and orbitrap fragment spectra data with two different labeled linkers DSS-d₀/d₁₂ and PDH-d₀/d₁₀. Identified cross-links that link residues covered by the PDB structure 4F5S were analyzed by TopoLink. The red bars are the proportion of URPs linking residues that are either not solvent accessible, or are farther away than 35 Å according to the SAS distance. OpenPepXL identified a total of 65 URPs in the DSS orbitrap data set, including three IWS links, all of them below a distance of 40 Å. It identified 22 URPs in the PDH orbitrap data set, including one IWS link with a distance of 59.3 Å. xQuest Identified 16 URPs in the PDH orbitrap data set, including 3 IWS links. It identified 21 URPs in the DSS orbitrap data set, including one IWS link. xQuest identified 9 URPs in the PDH ion trap data set and 57 URPs in the DSS ion trap data set, including one IWS link with a distance of 70.2 Å.