Setting up SanXot

There are two options for ratio calculation in ProteinClusterQuant that are configured by the property _performRatioIntegration _in the setup.properties file.
If that property is set to FALSE, or it is not found, the final peptide node ratios will be calculated as an Ion Count ratio (Rc) (see publication for more details) in case of isobaric isotopologues, or as the average of the individual quantitative ratios in case of any other quantitation technique.
If that property is set to TRUE, PCQ will use **SanXot ** in order to aggregate all the individual quantitative measurements, from PSMs (or from isotopologue ions in case of isotopologue quantitation) to peptide nodes, including the aggregation of the different technical and/or biological replicates. With this method, a weighted average is performed over each level in which the weight is inversely proportional to the variance of the values.

A copy of Windows executable files of SanXoT software package is available on request at jvazquez at cnic.es. (Jesús Vázquez Cobos Proteomics Laboratory, CNIC, Spain).

Note: SanXot windows executables have been tested successfully under Windows 7. However, there was some issues to running them under Windows 8 or up.

For more information about this method go to: Mol Cell Proteomics. 2011 Jan;10(1):M110.003335. doi: 10.1074/mcp.M110.003335. Epub 2010 Aug 31.

Here we show how to setup SanXot in the PCQ analysis software:

1. Once you have got the Windows executables, save them into a folder in the computer you are going to run PCQ, for example at 'c:\Users\myuser\SanXot'.
2. Which files should you have? You should have three 'exe' files: sanxot.exe, sanxotsieve.exe and klibrate.exe. Additionally you should have some dependency libraries.
3. In the analysis input parameter file, you may specify the following parameters as:
   • performRatioIntegration = TRUE
   • sanxotPath = c:\Users\myuser\SanXot
   • outliersRemovalFDR = 0.01
   • significantFDRThreshold = 0.05

Note 2: For running SanXot under a different platform you will need a compatible version of SanXot software, which may not be available for now (contact jvazquez at cnic.es in any case).

If you got the python scripts from jvazquez at cnic.es this are the required Python installations and dependencies

1. Download and install python 2.7.
2. Download (by right click and "save target") get-pip to local drive.
3. At the command prompt, navigate to the directory containing get-pip.py and run python get-pip.py which creates files in C:\Python27\Scripts, including pip2, pip2.7 and pip.
4. Still at the command prompt, go to C:\Python27\Scripts and run the following commands to install some required dependencies:
   • pip2.7.exe install numpy
   • pip2.7.exe install matplotlib
   • pip2.7.exe install scipy