#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/MzDataFile.h>
#include <OpenMS/FORMAT/PepXMLFile.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/CHEMISTRY/ResidueDB.h>
#include <OpenMS/CHEMISTRY/ResidueModification.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/ProteaseDB.h>
#include <OpenMS/FORMAT/MzIdentMLFile.h>
#include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h>
#include <OpenMS/FORMAT/DATAACCESS/MSDataCachedConsumer.h>
#include <QtCore/QDir>
#include <iostream>
#include <fstream>