Table of contents

1. Installation instructions
2. Testing the installation

Installation instructions

Before installing Shotgun Protein Sequencing:

• Matlab must be installed before using this package; details on the installation of Matlab can be found on Mathworks website.
• Compiling this package requires a standard C++ compiler - a Makefile is provided for GNU gcc.
• Support for mzXML files requires the Xerces-C library. Runtime binaries can be downloaded from the Xerces stable distribution.

Installing Shotgun Protein Sequencing

1. Edit the Makefile and change XERCES_ROOT to the directory where you installed the runtime binaries for Xerces-C. Also change CC if you're using a different compiler.
2. Run make
3. Add the Shotgun Protein Sequencing directory to Matlab's search path:
   • In Windows, choose the menu item "Set Path..." from the "File" menu.
   • In Unix, edit (or create) your startup.m file and use addpath.
4. In Unix, you may also need change the environment variable LD_LIBRARY_PATH to include the path to Xerces-C library files.

Testing the installation

1. cd to the directory containing the example data and parameters file (default is "cd c:\sps\example")
2. run "sps('example.params');"
3. see Results and Analysis for an explanation of how to interpret the results and parameterize the spectral networks analysis.