This directory contains the tools to prepare the input for the Matlab program. 

1: Extract and show MS1 data in Matlab.
In matlab, MS1 data can be extracted from mzXML file by following the example provided by"Example.m". 
Each scan will be named as "scan#.txt". To show one specrum:
data=load('scan#.txt');
plot(data(:, 1), data(:,2));
xlabel('mass to charge ratio');
ylabel('Intensity');
All codes are in directory "mzXMLReaderMatlab".

Note1: this tool depends on "org.apache.axis.encoding.Base64()" to perform base64 decoding. Some 
Matlab may not contain this toolkit. If this is the case, try the following ruby program.
Note2: Matlab reader will fail if each spectrum is compressed by "zlib". If this is the case (
i.g. compressionType="zlib" can be found in the mzXML file), try the following ruby program instead.

2: Ruby tools to prepare the input of our program.
Extract MS1 data, parse xtandem result and prepare the input for the regression model. An example
"AnalyzeMS.rb" is given to show how to use "RubyLib".