#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/MzDataFile.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/XTandemXMLFile.h>
#include <OpenMS/FORMAT/XTandemInfile.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
#include <OpenMS/CHEMISTRY/EnzymesDB.h>
#include <QtCore/QFile>
#include <QtCore/QProcess>
#include <QDir>
#include <fstream>