This application read MS spectra, apply filters and generate new file.
By now, it filters only msp/sptxt spectra with only one available filter JPLIntensityAttenuator.
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) 2.2 mz distributions at precursors neighborhood (from 1 to z) (example) END  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.