Quick User Guide
To test it you can use the test-files
delivered (test.fasta, test.mgf and test.ssf)
- Load a Fasta file containing the aminoacid sequence
by clicking "Load Fasta"-Button. The file name and directory are
- Load your Mass-Spec data in *.mgf, *.pkl, *.mzXML or *.mzML format.
Again, the file name is shown.
- You can change the settings of your analysis concerning Proteolysis,
Modifications, Neutral Losses, Cross-Linker, Accuracies and Mass
Limits, by clicking the "Settings"-Button.
- After clicking the "Start"-Button, a window pops up
that summarizes the settings used for calculation. If those settings
are ok, use the "OK"-Button to start analysis. Depending on the
sizes of the MS-Data file and Fasta-file as well as the settings used,
the analysis takes several seconds to minutes.
- When the analysis has finished, 2 windows will pop up: 1.)
the Main Analysis Window, showing all identified cross link
candidates 2.) the Decoy Window. The decoy analysis gives an
idea of the quality of the analysis.
- In the Main Analysis Window, select a candidate from
the table in th upper panel. This will show details of this
candidate in the lower 2 panels. On the left is a table giving the different
sites of cross linking that are possible between the 2 peptides and
a schematic representation of the fragmentation of the selected
precursor. The right panel shows the labeled spectrum. By
clicking on the "Details of Crosslink"-Button another window
will open, that shows all necessary information to evaluate a