MSDataFilter

This application read MS spectra, apply filters and generate new file.

BEGIN
1.  parse the file with spectra lib
2.  compute MS1/MS2 peaks distributions over all spectra (here is an example for precursor charge +3)
    [2 types of more local distributions through mz precursor intervals]
2.1 mz distributions of all mzs (example[1])
2.2 mz distributions at precursors neighborhood (from 1 to z) (example[1])
END

[1] these histograms are rendered (with R) with option -r (see command line below).
      

 usage: MSDataFilter <fasta> [-b <arg>] [--bp] [-e <arg>] [-g <arg>] [-h]
       [-i <arg>] [--no-norm] [-o <arg>] [-p <arg>] [-q] [-r] [-s <arg>] [-t
       <arg>] [-v]
       
 -b,--bin-width <arg>         set the width of interval in histograms
                              by default: 1.0.
    --bp <arg>                set base peak intensity for normalization
                              process.
 -e,--export-ratios <arg>     export ratios in filename
                              by default: null.
 -g,--group-number <arg>      set the number of peak list partitions by
                              precursor charge
                              by default: 10.
 -h,--help                    print this message.
 -i,--setting-file <arg>      give a property file with all input
                              settings.
    --no-norm                 disable base peak intensity normalization.
 -o,--output <arg>            set the output filename
                              by default: null.
 -p,--precision <arg>         define the decimal precision for any
                              mass-to-charge ratio
                              by default: 6.
 -q,--quiet                   quiet mode (verbose off).
 -r,--render                  export and render MS histograms in /tmp/hist
                              by default: false.
 -s,--sliding-window <arg>    set the sliding window value to compute
                              baseline histogram
                              by default: 20.
 -t,--threshold-ratio <arg>   set the ratio threshold for the attenuator
                              filter
                              by default: 2.0.
 -v,--version                 print the version info. 
      

The latest version is v0.2 - Download app with java sources.