After you perform the search, you can display the fragment match spectra in the Crosslink Spectrum Match Identification Details view. The application displays the fragment spectra in a separate dialog box, as shown in the next figure. The display differs, depending on the acquisition strategy that you used.
Procedure
- To open the Crosslink Spectrum Match Identification Details view, do the following:
- Double-click a CSM on the CSMs page of the result file.
The following figure shows a fragment spectrum acquired with the MS2_MS2_MS3 acquisition method. (See MS2_MS2_MS3 method.) An MS2 scan appears at the top of the view. The scan shows only crosslink reporter peaks.
The MS2 scan is used for detection. The MS3 scans are at the lower portion of the display. They represent crosslinked peptides, which are divided into four different masses: two pairs of masses for each peptide, with each pair differing by linker fragment mass.