Alexandre Masselot
and 1 contributors

NAME

getIonIntensities.pl - Extraction of ion intensities information from a .peptSpectra.xml file

SYNOPSIS

getIonIntensities.pl --pept=peptfile [options]

OPTIONS

Use getIonIntensities.pl -h

DESCRIPTION

The script parses a collection of trusted peptide/spectrum matches stored in a .peptSpectra.xml file to extract statistics regarding fragment ion intensities. It is possible to output the results either in text format (default) or in a format readable by R. In the latter case, the simple R script, ionStat.R, can be used for plotting data.

In addition, plots can be generated for each match found in the .peptSpectra.xml file(s) by using the -withplots.

EXAMPLE

./getIonIntensities.pl --pept=example.peptSpectra.xml -rformat -withplots > intensities.dataf

AUTHOR

Jacques Colinge