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Welcome to the xilmass wiki!

Xilmass is open-source and freely available under the permissive Apache2 license. Xilmass is platform free, therefore works on Windows, Linux and OS-X operating systems. Xilmass is implemented in Java and therefore, make sure that [JDK] (http://www.oracle.com/technetwork/java/javase/downloads/index.html) is already installed on your computer environment. The current program works as a standalone version which can be run by following the steps described underneath, as well as GUI.

This wiki consists of the following page:

1. Start up Xilmass: How to run Xilmass

2. Instructions to run a graphical user-interface (GUI) version for the identification of cross linked peptides

3. Instructions to run a command line (CLI) version for the identification of cross linked peptides

3.1. Xilmass parameters CLI

[3.2. Modifications] (https://github.com/compomics/xilmass/wiki/3.2.-Modifications)

4. Visualizing the Xilmass peptides-to-spectrum matches

5. Database