Figure 1.

In-source fragmentation data acquisition cycle and search strategy. (A) In an in-source experiment for crosslink detection, the declustering and/or desolvation source voltage setting is initially set at a typical value for the first high-resolution scan, to support the detection of the intact crosslinked peptide. In a second high-resolution scan, this source voltage is quickly increased to fragment the crosslinker for mass measurement of the component peptides. Subsequent MS² scans are performed at this elevated voltage to sequence the resulting fragmented peptides. (B) The peptides identified at the high source voltage setting are linked back to a potential crosslinked peptide using accurate masses from both MS¹ scans. The figure shows that chromatographic separation is required to resolve potential interferents.