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StavroX & MeroX

Tool for Identifying Cross-Linked Peptides with Mass Spectrometry

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Recent Version:
StavroX 3.6.6
MeroX 1.6.6

Quick User Guide

To test it you can use the test-files delivered (test.fasta, test.mgf and test.ssf)

  1. Load a Fasta file containing the aminoacid sequence by clicking "Load Fasta"-Button. The file name and directory are shown.
  2. Load your Mass-Spec data in *.mgf, *.pkl, *.mzXML or *.mzML format. Again, the file name is shown.
  3. You can change the settings of your analysis concerning Proteolysis, Modifications, Neutral Losses, Cross-Linker, Accuracies and Mass Limits, by clicking the "Settings"-Button.
    StavroX Start Window

    Start Window

  4. 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.
  5. 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.
    StavroX Main Window

    Main Analysis Window

    Decoy Window

    Decoy Window

  6. 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 correct cross-link.
    Detail Window

    Detail Window