#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CHEMISTRY/ProteaseDB.h>
#include <OpenMS/CHEMISTRY/ProteaseDigestion.h>
#include <OpenMS/CHEMISTRY/SpectrumAnnotator.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/MascotXMLFile.h>
#include <OpenMS/FORMAT/MzIdentMLFile.h>
#include <OpenMS/FORMAT/OMSFile.h>
#include <OpenMS/FORMAT/OMSSAXMLFile.h>
#include <OpenMS/FORMAT/PepXMLFile.h>
#include <OpenMS/FORMAT/PercolatorOutfile.h>
#include <OpenMS/FORMAT/ProtXMLFile.h>
#include <OpenMS/FORMAT/SequestOutfile.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <OpenMS/FORMAT/XQuestResultXMLFile.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/METADATA/ID/IdentificationDataConverter.h>
#include <OpenMS/FORMAT/XTandemXMLFile.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/SYSTEM/File.h>