#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/ANALYSIS/ID/PeptideIndexing.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/SYSTEM/File.h>