#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/CHEMISTRY/ProteaseDB.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/InspectInfile.h>
#include <OpenMS/FORMAT/InspectOutfile.h>
#include <OpenMS/FORMAT/MzXMLFile.h>
#include <OpenMS/FORMAT/PTMXMLFile.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <OpenMS/SYSTEM/File.h>
#include <cstdlib>
#include <vector>
#include <QtCore/QProcess>