#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/CHEMISTRY/ProteaseDB.h>
#include <OpenMS/CHEMISTRY/ProteaseDigestion.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMDecoy.h>
#include <OpenMS/CHEMISTRY/DigestionEnzyme.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/MATH/MISC/MathFunctions.h>
#include <OpenMS/DATASTRUCTURES/FASTAContainer.h>
#include <boost/regex.hpp>