1. Start up Xilmass
To start using Xilmass, unzip the downloaded file from here.
</br>
Xilmass can start identifying by double clicking over the xilmass-X.Y.Z.jar (X.Y.Z shows the current version number).
If that is not the case, please run a command prompt on a folder that contains xilmass-X.Y.Z.jar with following step.
On the command prompt:
to run the a graphical user-interface (GUI) version for the identification of cross-linked peptides in your sample:
java -jar Xilmass-X.Y.Z.jar
Follow the instruction here.
Further options to run Xilmass
Xilmass can be run as a command line which can be easily plug in your pipeline. Moreover, Xilmass can be also performed to visualize how experimental spectrum is annotated by Xilmass.
To achieve this, please run a command prompt on a folder that contains xilmass-X.Y.Z.jar with following step.
On the command prompt:
to run the command-line (CLI) version for the identification of cross-linked peptides in your sample:
java -jar Xilmass-X.Y.Z.jar -c
Follow the instruction [here] (https://github.com/compomics/xilmass/wiki/3.-Instructions-to-run-CLI-for-the-identification-of-cross-linked-peptides).
</br>
Please make sure that [resources/xLink.properties] (https://github.com/compomics/xilmass/wiki/3.1.-Xilmass-parameters-CLI) have the right settings.
</br>
</br>
to run GUI to inspect identified peptide-to-spectrum matches by Xilmass:
java -jar Xilmass-X.Y.Z.jar -r
Follow the instruction [here] (https://github.com/compomics/xilmass/wiki/4.-Visualizing-the-Xilmass-peptides-to-spectrum-matches).
</br>
</br>
</br>
Furthermore, there are other parameters with following functionalities:
java -jar Xilmass-X.Y.Z.jar -h
to provide information for the available commands.
</br>