#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/CHEMISTRY/ProteaseDB.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideHit.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/SpectrumLookup.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/MascotGenericFile.h>
#include <OpenMS/FORMAT/CsvFile.h>
#include <OpenMS/FORMAT/DATAACCESS/MSDataTransformingConsumer.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/SYSTEM/JavaInfo.h>
#include <QFileInfo>
#include <fstream>