diff --git a/src/openms/source/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabet.cpp b/src/openms/source/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabet.cpp
index 5ebaeb8fe2a..392140c504b 100644
--- a/src/openms/source/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabet.cpp
+++ b/src/openms/source/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabet.cpp
@@ -41,12 +41,9 @@
 #include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabet.h>
 #include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabetTextParser.h>
 
-namespace OpenMS
+namespace OpenMS::ims
 {
 
-  namespace ims
-  {
-
     const IMSAlphabet::name_type & IMSAlphabet::getName(size_type index) const
     {
       return getElement(index).getName();
@@ -174,5 +171,4 @@ namespace OpenMS
       return os;
     }
 
-  } // namespace ims
-} // namespace OpenMS
+} // namespace OpenMS // namespace ims
diff --git a/src/openms/source/COMPARISON/SPECTRA/BinnedSpectrum.cpp b/src/openms/source/COMPARISON/SPECTRA/BinnedSpectrum.cpp
index c94d1127a65..9b086e5de33 100644
--- a/src/openms/source/COMPARISON/SPECTRA/BinnedSpectrum.cpp
+++ b/src/openms/source/COMPARISON/SPECTRA/BinnedSpectrum.cpp
@@ -81,7 +81,10 @@ namespace OpenMS
   {
     OPENMS_PRECONDITION(ps.isSorted(), "Spectrum needs to be sorted by m/z.");
 
-    if (ps.empty()) { return; }
+    if (ps.empty())
+    { 
+      return;
+    }
 
     bins_ = EmptySparseVector;
 
@@ -120,15 +123,20 @@ namespace OpenMS
     }
 
     // efficient look-up of number of non-zero entries, so we use this as-well
-    if (bins_.nonZeros() != rhs.bins_.nonZeros()) { return false; }
+    if (bins_.nonZeros() != rhs.bins_.nonZeros())
+    {
+      return false;
+    }
 
     // test non-sparse (non-zero) elements for equality
     SparseVectorIteratorType it(bins_);
     SparseVectorIteratorType rhs_it(rhs.bins_);  
     while (it)      
     {
-      if (it.index() != rhs_it.index()
-       || it.value() != rhs_it.value()) { return false; }
+      if (it.index() != rhs_it.index() || it.value() != rhs_it.value())
+      {
+        return false;
+      }
       ++it;
       ++rhs_it;
     }
diff --git a/src/openms/source/COMPARISON/SPECTRA/PeakAlignment.cpp b/src/openms/source/COMPARISON/SPECTRA/PeakAlignment.cpp
index 6caddb4a2fe..ec995e1c8aa 100644
--- a/src/openms/source/COMPARISON/SPECTRA/PeakAlignment.cpp
+++ b/src/openms/source/COMPARISON/SPECTRA/PeakAlignment.cpp
@@ -85,10 +85,14 @@ namespace OpenMS
     // shortcut similarity calculation by comparing PrecursorPeaks (PrecursorPeaks more than delta away from each other are supposed to be from another peptide)
     double pre_mz1 = 0.0;
     if (!spec1.getPrecursors().empty())
+    {
       pre_mz1 = spec1.getPrecursors()[0].getMZ();
+    }
     double pre_mz2 = 0.0;
     if (!spec2.getPrecursors().empty())
+    {
       pre_mz2 = spec2.getPrecursors()[0].getMZ();
+    }
     if (fabs(pre_mz1 - pre_mz2) > (double)param_.getValue("precursor_mass_tolerance"))
     {
       return 0;
diff --git a/src/openms/source/COMPARISON/SPECTRA/SpectrumAlignmentScore.cpp b/src/openms/source/COMPARISON/SPECTRA/SpectrumAlignmentScore.cpp
index 87bfd8dad25..07255de7fcf 100644
--- a/src/openms/source/COMPARISON/SPECTRA/SpectrumAlignmentScore.cpp
+++ b/src/openms/source/COMPARISON/SPECTRA/SpectrumAlignmentScore.cpp
@@ -97,11 +97,16 @@ namespace OpenMS
     
     // calculate sum of squared intensities
     double sum1(0);
-    for (auto const & p : s1) { sum1 += pow(p.getIntensity(), 2); }
+    for (auto const & p : s1)
+    { 
+      sum1 += pow(p.getIntensity(), 2);
+    }
 
     double sum2(0);
-    for (auto const & p : s2) { sum2 += pow(p.getIntensity(), 2); }
-
+    for (auto const & p : s2)
+    { 
+      sum2 += pow(p.getIntensity(), 2);
+    }
     for (auto const & ap : alignment)
     {
       const double mz_tolerance = is_relative_tolerance ? tolerance * s1[ap.first].getMZ() * 1e-6 : tolerance;
diff --git a/src/openms/source/COMPARISON/SPECTRA/SpectrumCheapDPCorr.cpp b/src/openms/source/COMPARISON/SPECTRA/SpectrumCheapDPCorr.cpp
index e1b9635c7d0..d5b397d4ff0 100644
--- a/src/openms/source/COMPARISON/SPECTRA/SpectrumCheapDPCorr.cpp
+++ b/src/openms/source/COMPARISON/SPECTRA/SpectrumCheapDPCorr.cpp
@@ -111,9 +111,13 @@ namespace OpenMS
     lastconsensus_ = PeakSpectrum();
     Precursor p1, p2;
     if (!x.getPrecursors().empty())
+    {
       p1 = x.getPrecursors()[0];
+    }
     if (!y.getPrecursors().empty())
+    {
       p2 = y.getPrecursors()[0];
+    }
     lastconsensus_.getPrecursors().resize(1);
     lastconsensus_.getPrecursors()[0].setMZ((p1.getMZ() + p2.getMZ()) / 2);
     lastconsensus_.getPrecursors()[0].setCharge(p1.getCharge());
@@ -174,9 +178,13 @@ namespace OpenMS
             yrun++;
           }
           if (xit + xrun == x.end())
+          {
             break;
+          }
           if (yit + yrun == y.end())
+          {
             break;
+          }
         }
 
         //dynamic programming necessary to calculate optimal pairing
@@ -292,7 +300,9 @@ namespace OpenMS
         consensuspeak.setMZ(x[xstart + i - 1].getMZ());
         consensuspeak.setIntensity((x[xstart + i - 1].getIntensity()) * (1 - factor_));
         if (keeppeaks_)
+        {
           lastconsensus_.push_back(consensuspeak);
+        }
         i--;
       }
       else if (trace[i][j] == -1)
@@ -301,11 +311,15 @@ namespace OpenMS
         consensuspeak.setMZ(y[ystart + j - 1].getMZ());
         consensuspeak.setIntensity((y[ystart + j - 1].getIntensity()) * factor_);
         if (keeppeaks_)
+        {
           lastconsensus_.push_back(consensuspeak);
+        }
         j--;
       }
       if (!i || !j)
+      {
         break;
+      }
     }
 
     return dparray[xend - xstart + 1][yend - ystart + 1];
diff --git a/src/openms/source/COMPARISON/SPECTRA/SpectrumPrecursorComparator.cpp b/src/openms/source/COMPARISON/SPECTRA/SpectrumPrecursorComparator.cpp
index 2e8e89954d7..0a082743dfa 100644
--- a/src/openms/source/COMPARISON/SPECTRA/SpectrumPrecursorComparator.cpp
+++ b/src/openms/source/COMPARISON/SPECTRA/SpectrumPrecursorComparator.cpp
@@ -78,10 +78,14 @@ namespace OpenMS
 
     double mz1 = 0.0;
     if (!x.getPrecursors().empty())
+    {
       mz1 = x.getPrecursors()[0].getMZ();
+    }
     double mz2 = 0.0;
     if (!y.getPrecursors().empty())
+    {
       mz2 = y.getPrecursors()[0].getMZ();
+    }
 
     if (fabs(mz1 - mz2) > window)
     {
diff --git a/src/openms/source/COMPARISON/SPECTRA/SteinScottImproveScore.cpp b/src/openms/source/COMPARISON/SPECTRA/SteinScottImproveScore.cpp
index e8bfc9fe321..9d995d999f9 100644
--- a/src/openms/source/COMPARISON/SPECTRA/SteinScottImproveScore.cpp
+++ b/src/openms/source/COMPARISON/SPECTRA/SteinScottImproveScore.cpp
@@ -103,16 +103,16 @@ namespace OpenMS
     std::cout << std::endl;
     std::cout << s2 << std::endl;*/
 
-    for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
+    for (const Peak1D& it1 : s1)
     {
-      double temp = it1->getIntensity();
+      double temp = it1.getIntensity();
       sum1 += temp * temp;
       sum3 += temp;
     }
 
-    for (PeakSpectrum::ConstIterator it1 = s2.begin(); it1 != s2.end(); ++it1)
+    for (const Peak1D& it1 : s2)
     {
-      double temp = it1->getIntensity();
+      double temp = it1.getIntensity();
       sum2 += temp * temp;
       sum4 += temp;
     }
diff --git a/src/openms/source/COMPARISON/SPECTRA/ZhangSimilarityScore.cpp b/src/openms/source/COMPARISON/SPECTRA/ZhangSimilarityScore.cpp
index 1734b3d8053..38e4f6c5676 100644
--- a/src/openms/source/COMPARISON/SPECTRA/ZhangSimilarityScore.cpp
+++ b/src/openms/source/COMPARISON/SPECTRA/ZhangSimilarityScore.cpp
@@ -93,9 +93,9 @@ namespace OpenMS
       throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
     }
 
-    for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
+    for (const Peak1D& it1 : s1)
     {
-      sum1 += it1->getIntensity();
+      sum1 += it1.getIntensity();
       /*
 for (PeakSpectrum::ConstIterator it2 = s1.begin(); it2 != s1.end(); ++it2)
 {
@@ -158,9 +158,9 @@ for (PeakSpectrum::ConstIterator it2 = s1.begin(); it2 != s1.end(); ++it2)
       }
     }*/
 
-    for (PeakSpectrum::ConstIterator it1 = s2.begin(); it1 != s2.end(); ++it1)
+    for (const Peak1D& it1 : s2)
     {
-      sum2 += it1->getIntensity();
+      sum2 += it1.getIntensity();
       /*
 for (PeakSpectrum::ConstIterator it2 = s2.begin(); it2 != s2.end(); ++it2)
 {
diff --git a/src/openms/source/CONCEPT/ClassTest.cpp b/src/openms/source/CONCEPT/ClassTest.cpp
index 07481f7d80d..2f309c951d5 100644
--- a/src/openms/source/CONCEPT/ClassTest.cpp
+++ b/src/openms/source/CONCEPT/ClassTest.cpp
@@ -55,12 +55,9 @@
 
 #include <QFileInfo>
 
-namespace OpenMS
+namespace OpenMS::Internal::ClassTest
 {
-  namespace Internal
-  {
-    namespace ClassTest
-    {
+
       bool all_tests = true;
       bool equal_files;
       bool newline = false;
@@ -91,10 +88,6 @@ namespace OpenMS
       std::vector<std::string> tmp_file_list;
       std::vector<UInt> failed_lines_list;
       StringList whitelist;
-    }
-
-    namespace ClassTest
-    {
 
       void mainInit(const char* version, const char* class_name, int argc, const char* argv0)
       {
@@ -443,8 +436,7 @@ namespace OpenMS
         }
       }
 
-      bool
-      isRealSimilar(long double number_1, long double number_2)
+      bool isRealSimilar(long double number_1, long double number_2)
       {
         // Note: The original version of the stuff below was copied from
         // FuzzyStringComparator and then heavily modified for ClassTest.
@@ -571,8 +563,7 @@ namespace OpenMS
         }
       }
 
-      void
-      testStringEqual(const char* /*file*/, int line,
+      void testStringEqual(const char* /*file*/, int line,
                       const std::string& string_1,
                       const char* string_1_stringified,
                       const std::string& string_2,
@@ -684,7 +675,4 @@ namespace OpenMS
 
         return result;
       }
-
-    }
-  }
 }
diff --git a/src/openms/source/CONCEPT/FuzzyStringComparator.cpp b/src/openms/source/CONCEPT/FuzzyStringComparator.cpp
index 2b7df499e8f..b827271a6ed 100644
--- a/src/openms/source/CONCEPT/FuzzyStringComparator.cpp
+++ b/src/openms/source/CONCEPT/FuzzyStringComparator.cpp
@@ -300,8 +300,10 @@ namespace OpenMS
   bool FuzzyStringComparator::compareLines_(std::string const& line_str_1, std::string const& line_str_2)
   {
     // in most cases, results will be identical. If not, do the expensive fuzzy compare
-    if (line_str_1 == line_str_2) return true;
-    
+    if (line_str_1 == line_str_2)
+    {
+      return true;
+    }
     for (StringList::const_iterator slit = whitelist_.begin();
          slit != whitelist_.end(); ++slit)
     {
@@ -350,8 +352,10 @@ namespace OpenMS
 #ifdef DEBUG_FUZZY
             std::cout << "cmp number: " << String(element_1_.number) << " : " << String(element_2_.number) << std::endl;
 #endif
-            if (element_1_.number == element_2_.number) continue;
-
+            if (element_1_.number == element_2_.number)
+            {
+              continue;
+            }
             // check if absolute difference is small
             double absdiff = element_1_.number - element_2_.number;
             if (absdiff < 0)
@@ -666,7 +670,9 @@ namespace OpenMS
            wlcit != whitelist_cases_.end(); ++wlcit)
       {
         if (wlcit->first.size() > length)
+        {
           length = wlcit->first.size();
+        }
       }
       for (std::map<String, UInt>::const_iterator wlcit = whitelist_cases_.begin();
            wlcit != whitelist_cases_.end(); ++wlcit)
diff --git a/src/openms/source/CONCEPT/GlobalExceptionHandler.cpp b/src/openms/source/CONCEPT/GlobalExceptionHandler.cpp
index edeb7d9b728..d6a1e0cc27d 100644
--- a/src/openms/source/CONCEPT/GlobalExceptionHandler.cpp
+++ b/src/openms/source/CONCEPT/GlobalExceptionHandler.cpp
@@ -53,12 +53,9 @@
 
 #define OPENMS_CORE_DUMP_ENVNAME "OPENMS_DUMP_CORE"
 
-namespace OpenMS
+namespace OpenMS::Exception
 {
 
-  namespace Exception
-  {
-
     GlobalExceptionHandler::GlobalExceptionHandler() throw()
     {
       std::set_terminate(terminate);
@@ -143,6 +140,5 @@ namespace OpenMS
       GlobalExceptionHandler::line_() = line;
     }
 
-  } // namespace Exception
 
-} // namespace OpenMS
+} // namespace OpenMS // namespace Exception
diff --git a/src/openms/source/CONCEPT/Init.cpp b/src/openms/source/CONCEPT/Init.cpp
index 888851fa582..6c7e9c0bb88 100644
--- a/src/openms/source/CONCEPT/Init.cpp
+++ b/src/openms/source/CONCEPT/Init.cpp
@@ -36,28 +36,25 @@
 
 #include <xercesc/util/PlatformUtils.hpp>
 
-namespace OpenMS
+namespace OpenMS::Internal
 {
-  namespace Internal
-  {
 
-    // Initialize xerces
-    // see ticket #352 for more details
-    struct xerces_init
+  // Initialize xerces
+  // see ticket #352 for more details
+  struct xerces_init
+  {
+    xerces_init() 
     {
-      xerces_init() 
-      {
-        xercesc::XMLPlatformUtils::Initialize();
-      }
+      xercesc::XMLPlatformUtils::Initialize();
+    }
 
-      ~xerces_init() 
-      {
-        xercesc::XMLPlatformUtils::Terminate();
-      }
+    ~xerces_init() 
+    {
+      xercesc::XMLPlatformUtils::Terminate();
+    }
 
-    };
-    const xerces_init xinit;
+  };
+  const xerces_init xinit;
 
-  }
-}
+} //OpenMS //Internal
 
diff --git a/src/openms/source/CONCEPT/LogStream.cpp b/src/openms/source/CONCEPT/LogStream.cpp
index 88cb537fd42..78b1c47d335 100644
--- a/src/openms/source/CONCEPT/LogStream.cpp
+++ b/src/openms/source/CONCEPT/LogStream.cpp
@@ -82,7 +82,9 @@ namespace OpenMS
       {
         clearCache();
         if (incomplete_line_.size() > 0)
+        {
           distribute_(incomplete_line_);
+        }
         delete[] pbuf_;
         pbuf_ = nullptr;
       }
@@ -293,8 +295,9 @@ namespace OpenMS
 
                 // send outline (and extra_message) to attached streams
                 if (!extra_message.empty())
+                {
                   distribute_(extra_message);
-
+                }
                 distribute_(outstring);
               }
 
@@ -413,8 +416,9 @@ namespace OpenMS
     {
 
       if (registered_at_ == nullptr)
+      {
         return;
-
+      }
       registered_at_->remove(stream_);
       registered_at_ = nullptr;
     }
@@ -479,8 +483,9 @@ namespace OpenMS
     void LogStream::insertNotification(std::ostream & s, LogStreamNotifier & target)
     {
       if (!bound_())
+      {
         return;
-
+      }
       insert(s);
 
       StreamIterator it = findStream_(s);
@@ -504,16 +509,18 @@ namespace OpenMS
     bool LogStream::hasStream_(std::ostream & stream)
     {
       if (!bound_())
+      {
         return false;
-
+      }
       return findStream_(stream) != rdbuf()->stream_list_.end();
     }
 
     void LogStream::setPrefix(const std::ostream & s, const string & prefix)
     {
       if (!bound_())
+      {
         return;
-
+      }
       StreamIterator it = findStream_(s);
       if (it != rdbuf()->stream_list_.end())
       {
@@ -524,8 +531,9 @@ namespace OpenMS
     void LogStream::setPrefix(const string & prefix)
     {
       if (!bound_())
+      {
         return;
-
+      }
       for (StreamIterator it = rdbuf()->stream_list_.begin(); it != rdbuf()->stream_list_.end(); ++it)
       {
         (*it).prefix = prefix;
diff --git a/src/openms/source/CONCEPT/ProgressLogger.cpp b/src/openms/source/CONCEPT/ProgressLogger.cpp
index d23636f8903..357019b2e9b 100644
--- a/src/openms/source/CONCEPT/ProgressLogger.cpp
+++ b/src/openms/source/CONCEPT/ProgressLogger.cpp
@@ -174,11 +174,17 @@ namespace OpenMS
     switch (type)
     {
       case NONE:
+      {
         return "NONE";
+      }
       case CMD:
+      {
         return "CMD";
+      }
       case GUI:
+      {
         return "GUI";
+      }
     }
 
 // should never happen but gcc emits a warning/error
@@ -205,7 +211,10 @@ namespace OpenMS
 
   ProgressLogger& ProgressLogger::operator=(const ProgressLogger& other)
   {
-    if (&other == this) return *this;
+    if (&other == this)
+    {
+      return *this;
+    }
 
     this->last_invoke_ = other.last_invoke_;
     this->type_ = other.type_;
@@ -249,8 +258,10 @@ namespace OpenMS
   void ProgressLogger::setProgress(SignedSize value) const
   {
     // update only if at least 1 second has passed
-    if (last_invoke_ == time(nullptr)) return;
-
+    if (last_invoke_ == time(nullptr))
+    {
+      return;
+    }
     last_invoke_ = time(nullptr);
     current_logger_->setProgress(value, recursion_depth_);
   }
@@ -258,7 +269,10 @@ namespace OpenMS
   {
     auto p = current_logger_->nextProgress();
     // update only if at least 1 second has passed
-    if (last_invoke_ == time(nullptr)) return;
+    if (last_invoke_ == time(nullptr))
+    {
+      return;
+    }
 
     last_invoke_ = time(nullptr);
     current_logger_->setProgress(p, recursion_depth_);
diff --git a/src/openms/source/CONCEPT/Types.cpp b/src/openms/source/CONCEPT/Types.cpp
index a6b879157ca..b3d82fd8e00 100644
--- a/src/openms/source/CONCEPT/Types.cpp
+++ b/src/openms/source/CONCEPT/Types.cpp
@@ -35,10 +35,7 @@
 #include <OpenMS/CONCEPT/Types.h>
 #include <clocale>
 
-namespace OpenMS
+namespace OpenMS::Internal
 {
-  namespace Internal
-  {
-    const char * OpenMS_locale = setlocale(LC_ALL, "C");
-  }
-}
+  const char * OpenMS_locale = setlocale(LC_ALL, "C");  
+} // OpenMS // Internal
diff --git a/src/openms/source/CONCEPT/UniqueIdInterface.cpp b/src/openms/source/CONCEPT/UniqueIdInterface.cpp
index e77cbe91302..f78030df9f0 100644
--- a/src/openms/source/CONCEPT/UniqueIdInterface.cpp
+++ b/src/openms/source/CONCEPT/UniqueIdInterface.cpp
@@ -37,8 +37,7 @@
 namespace OpenMS
 {
 
-  void
-  UniqueIdInterface::setUniqueId(const String & rhs)
+  void UniqueIdInterface::setUniqueId(const String & rhs)
   {
     clearUniqueId();
 
diff --git a/src/openms/source/DATASTRUCTURES/Compomer.cpp b/src/openms/source/DATASTRUCTURES/Compomer.cpp
index 127e49e449a..d805f13084e 100644
--- a/src/openms/source/DATASTRUCTURES/Compomer.cpp
+++ b/src/openms/source/DATASTRUCTURES/Compomer.cpp
@@ -237,16 +237,18 @@ namespace OpenMS
   String Compomer::getAdductsAsString(UInt side) const
   {
     if (side >= BOTH)
+    {
       throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Compomer::getAdductsAsString() does not support this value for 'side'!", String(side));
-
+    }
     String r;
     for (const auto& [formula, adduct] : cmp_[side])
     {
       Int f = adduct.getAmount();
 
       if (formula.has('+'))
+      {
         throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "An Adduct contains implicit charge. This is not allowed!", formula);
-
+      }
       EmpiricalFormula ef(formula);
       ef = ef * f;
       r += ef.toString();
@@ -258,8 +260,9 @@ namespace OpenMS
   bool Compomer::isSingleAdduct(Adduct& a, const UInt side) const
   {
     if (side >= BOTH)
+    {
       throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Compomer::isSimpleAdduct() does not support this value for 'side'!", String(side));
-
+    }
     if (cmp_[side].size() != 1)
     {
       return false;
@@ -281,8 +284,9 @@ namespace OpenMS
   Compomer Compomer::removeAdduct(const Adduct& a, const UInt side) const
   {
     if (side >= BOTH)
+    {
       throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Compomer::removeAdduct() does not support this value for 'side'!", String(side));
-
+    }
     Compomer tmp(*this);
     if (tmp.cmp_[side].count(a.getFormula()) > 0)
     {
@@ -307,8 +311,9 @@ namespace OpenMS
   StringList Compomer::getLabels(const UInt side) const
   {
     if (side >= BOTH)
+    {
       throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Compomer::getLabels() does not support this value for 'side'!", String(side));
-
+    }
     StringList tmp;
 
     for (CompomerSide::const_iterator it = this->cmp_[side].begin(); it != this->cmp_[side].end(); ++it)
diff --git a/src/openms/source/DATASTRUCTURES/ConvexHull2D.cpp b/src/openms/source/DATASTRUCTURES/ConvexHull2D.cpp
index db63e356026..c20e9a89265 100644
--- a/src/openms/source/DATASTRUCTURES/ConvexHull2D.cpp
+++ b/src/openms/source/DATASTRUCTURES/ConvexHull2D.cpp
@@ -244,8 +244,9 @@ namespace OpenMS
     }
     compressed_map[middle_it->first] = middle_it->second; // copy last scan
     if (succ_it != map_points_.end())
+    {
       throw Exception::BufferOverflow(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
-
+    }
     //std::cout << "compressed CH from " << map_points_.size() << " to " << compressed_map.size() << "\n";
     Size saved_points = map_points_.size() - compressed_map.size();
     //copy
diff --git a/src/openms/source/FILTERING/CALIBRATION/InternalCalibration.cpp b/src/openms/source/FILTERING/CALIBRATION/InternalCalibration.cpp
index 1a5b007cf36..af2606f0c89 100644
--- a/src/openms/source/FILTERING/CALIBRATION/InternalCalibration.cpp
+++ b/src/openms/source/FILTERING/CALIBRATION/InternalCalibration.cpp
@@ -145,7 +145,10 @@ namespace OpenMS
             Size s_left = it->findNearest(mz_iso_left);
             if (Math::getPPMAbs(mz_iso_left, (*it)[s_left].getMZ()) < 0.5) // intra-scan ppm should be very good!
             { // peak nearby lock mass was not the monoisotopic
-              if (verbose) OPENMS_LOG_INFO << "peak at [RT, m/z] " << it->getRT() << ", " << (*it)[s].getMZ() << " is NOT monoisotopic. Skipping it!\n";
+              if (verbose)
+              {
+                OPENMS_LOG_INFO << "peak at [RT, m/z] " << it->getRT() << ", " << (*it)[s].getMZ() << " is NOT monoisotopic. Skipping it!\n";
+              }
               failed_lock_masses.insertCalibrationPoint(it->getRT(), itl->mz, 1.0, itl->mz, 0.0, std::distance(ref_masses.begin(), itl));
               continue;
             }
@@ -157,7 +160,10 @@ namespace OpenMS
             Size s_right = it->findNearest(mz_iso_right);
             if (!(Math::getPPMAbs(mz_iso_right, (*it)[s_right].getMZ()) < 0.5)) // intra-scan ppm should be very good!
             { // peak has no +1iso.. weird
-              if (verbose) OPENMS_LOG_INFO << "peak at [RT, m/z] " << it->getRT() << ", " << (*it)[s].getMZ() << " has no +1 isotope (ppm to closest: " << Math::getPPM(mz_iso_right, (*it)[s_right].getMZ()) << ")... Skipping it!\n";
+              if (verbose)
+              {
+                OPENMS_LOG_INFO << "peak at [RT, m/z] " << it->getRT() << ", " << (*it)[s].getMZ() << " has no +1 isotope (ppm to closest: " << Math::getPPM(mz_iso_right, (*it)[s_right].getMZ()) << ")... Skipping it!\n";
+              }
               failed_lock_masses.insertCalibrationPoint(it->getRT(), itl->mz, 2.0, itl->mz, 0.0, std::distance(ref_masses.begin(), itl));
               continue;
             }
@@ -261,8 +267,14 @@ namespace OpenMS
     double delta = Math::getPPMAbs(mz_obs, mz_ref);
     if (tol_ppm < delta)
     {
-      if (stats.cnt_decal < 10) OPENMS_LOG_INFO << "Peptide " << pid.getHits()[0].getSequence().toString() << " is " << delta << " (>" << tol_ppm << ") ppm away from theoretical mass and is omitted as calibration point.\n";
-      else if (stats.cnt_decal == 10) OPENMS_LOG_INFO << "More than 10 peptides are at least " << tol_ppm << " ppm away from theoretical mass and are omitted as calibration point.";
+      if (stats.cnt_decal < 10)
+      {
+        OPENMS_LOG_INFO << "Peptide " << pid.getHits()[0].getSequence().toString() << " is " << delta << " (>" << tol_ppm << ") ppm away from theoretical mass and is omitted as calibration point.\n";
+      }
+      else if (stats.cnt_decal == 10)
+      {
+        OPENMS_LOG_INFO << "More than 10 peptides are at least " << tol_ppm << " ppm away from theoretical mass and are omitted as calibration point.";
+      }
       ++stats.cnt_decal;
       return true;
     }
@@ -439,9 +451,18 @@ namespace OpenMS
         for (Size i = 0; i < tms.size(); ++i)
         {
           sv << tms[i].getRT() << tms[i].toString();
-          if (!MZTrafoModel::isValidModel(tms[i])) sv << "invalid"; // this only happens if ALL models are invalid (since otherwise they would use 'neighbour')
-          else if (invalid_models.count(i) > 0) sv << "neighbor";
-          else sv << "local";
+          if (!MZTrafoModel::isValidModel(tms[i]))
+          {
+            sv << "invalid"; // this only happens if ALL models are invalid (since otherwise they would use 'neighbour')
+          }
+          else if (invalid_models.count(i) > 0)
+          {
+            sv << "neighbor";
+          }
+          else 
+          {
+            sv << "local";
+          }
           sv << nl;
         }
       }
@@ -473,8 +494,11 @@ namespace OpenMS
     std::vector<double> vec_ppm_before, vec_ppm_after;
     vec_ppm_before.reserve(cal_data_.size());
     vec_ppm_after.reserve(cal_data_.size());
-    if (sv != nullptr) *sv << "# residual error after calibration" << nl
+    if (sv != nullptr)
+    {
+      *sv << "# residual error after calibration" << nl
                         << "RT" << "intensity" << "mz ref" << "mz before" << "mz after" << "ppm before" << "ppm after" << nl;
+    }
     Size ii(0);
     for (CalibrationData::const_iterator itc = cal_data_.begin(); itc != cal_data_.end(); ++itc, ++ii)
     {
@@ -483,7 +507,10 @@ namespace OpenMS
       Size idx = (global_model ? 0 : MZTrafoModel::findNearest(tms, rt));
 
       double mz_corrected = std::numeric_limits<double>::quiet_NaN();
-      if (MZTrafoModel::isValidModel(tms[idx])) mz_corrected = tms[idx].predict(itc->getMZ());
+      if (MZTrafoModel::isValidModel(tms[idx]))
+      {
+        mz_corrected = tms[idx].predict(itc->getMZ());
+      }
       double mz_ref = cal_data_.getRefMZ(ii);
       double ppm_before = Math::getPPM(itc->getMZ(), mz_ref);
       double ppm_after = Math::getPPM(mz_corrected, mz_ref);
@@ -517,8 +544,10 @@ namespace OpenMS
     if (!hasValidModels)
     { // QC tables are done; quit
       OPENMS_LOG_ERROR << "Error: Could not build a single local calibration model! Check your calibrants and/or extend the search window!" << std::endl;
-      if (use_RANSAC) OPENMS_LOG_ERROR << "       Since you are using RANSAC, check the parameters as well and test different setups." << std::endl;
-
+      if (use_RANSAC)
+      {
+        OPENMS_LOG_ERROR << "       Since you are using RANSAC, check the parameters as well and test different setups." << std::endl;
+      }
       return false;
     }
 
diff --git a/src/openms/source/FILTERING/CALIBRATION/MZTrafoModel.cpp b/src/openms/source/FILTERING/CALIBRATION/MZTrafoModel.cpp
index 70c6f2fef6c..dcc10f933f0 100644
--- a/src/openms/source/FILTERING/CALIBRATION/MZTrafoModel.cpp
+++ b/src/openms/source/FILTERING/CALIBRATION/MZTrafoModel.cpp
@@ -102,10 +102,18 @@ namespace OpenMS
     if (trafo.coeff_.empty()) return false;
 
     // go through coefficients and see if they are too extreme
-    if (limit_offset_ < fabs(trafo.coeff_[0])) return false;
-    if (limit_scale_ < fabs(trafo.coeff_[1])) return false;
-    if (limit_power_ < fabs(trafo.coeff_[2])) return false;
-
+    if (limit_offset_ < fabs(trafo.coeff_[0]))
+    {
+      return false;
+    }
+    if (limit_scale_ < fabs(trafo.coeff_[1]))
+    {
+      return false;
+    }
+    if (limit_power_ < fabs(trafo.coeff_[2]))
+    {
+      return false;
+    }
     return (true);
   }
 
@@ -197,8 +205,10 @@ namespace OpenMS
     {
       if (md == LINEAR)
       {
-        if (obs_mz.size() < 2) return false;
-
+        if (obs_mz.size() < 2)
+        {
+          return false;
+        }
         if (use_RANSAC && 
           (obs_mz.size() > ransac_params_->n)) // with fewer points, RANSAC will fail
         {
@@ -230,8 +240,10 @@ namespace OpenMS
       }
       else if (md == LINEAR_WEIGHTED)
       {
-        if (obs_mz.size() < 2) return false;
-
+        if (obs_mz.size() < 2)
+        {
+          return false;
+        }
         double confidence_interval_P(0.0);
         Math::LinearRegression lr;
         lr.computeRegressionWeighted(confidence_interval_P, theo_mz.begin(), theo_mz.end(), obs_mz.begin(), weights.begin(), false);
@@ -241,8 +253,10 @@ namespace OpenMS
       }
       else if (md == QUADRATIC)
       {
-        if (obs_mz.size() < 3) return false;
-
+        if (obs_mz.size() < 3)
+        {
+          return false;
+        }
         if (use_RANSAC && 
           (obs_mz.size() > ransac_params_->n)) // with fewer points, RANSAC will fail
         {
@@ -270,8 +284,10 @@ namespace OpenMS
       }
       else if (md == QUADRATIC_WEIGHTED)
       {
-        if (obs_mz.size() < 3) return false;
-
+        if (obs_mz.size() < 3)
+        {
+          return false;
+        }
         // Quadratic fit (weighted)
         Math::QuadraticRegression qr;
         qr.computeRegressionWeighted(theo_mz.begin(), theo_mz.end(), obs_mz.begin(), weights.begin());
@@ -292,12 +308,19 @@ namespace OpenMS
       std::vector<double> st_ppm_before, st_ppm_after;
       for (Size i = 0; i < obs_mz.size(); i++)
       {
-        if (use_ppm_) st_ppm_before.push_back(obs_mz[i]);
-        else st_ppm_before.push_back(Math::getPPM(theo_mz[i], obs_mz[i]));
-
+        if (use_ppm_)
+        {
+          st_ppm_before.push_back(obs_mz[i]);
+        }
+        else 
+        {
+          st_ppm_before.push_back(Math::getPPM(theo_mz[i], obs_mz[i]));
+        }
         double obs_mz_v = obs_mz[i];
-        if (use_ppm_) obs_mz_v = Math::ppmToMass(obs_mz_v, theo_mz[i]) + theo_mz[i]; //
-
+        if (use_ppm_)
+        {
+          obs_mz_v = Math::ppmToMass(obs_mz_v, theo_mz[i]) + theo_mz[i];
+        }
         st_ppm_after.push_back(Math::getPPM(theo_mz[i], predict(obs_mz_v))); // predict() is ppm-aware itself
 
         printf("%4.5f  %4.5f  %2.1f | %2.1f\n", theo_mz[i], obs_mz_v, st_ppm_before.back(), st_ppm_after.back());
@@ -379,8 +402,10 @@ namespace OpenMS
 
   void MZTrafoModel::getCoefficients( double& intercept, double& slope, double& power )
   {
-    if (!isTrained()) throw Exception::Precondition(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Model is not trained yet.");
-
+    if (!isTrained())
+    {
+      throw Exception::Precondition(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Model is not trained yet.");
+    }
     intercept = coeff_[0];
     slope = coeff_[1];
     power = coeff_[2];
diff --git a/src/openms/source/FILTERING/CALIBRATION/PrecursorCorrection.cpp b/src/openms/source/FILTERING/CALIBRATION/PrecursorCorrection.cpp
index 33330092d07..474ae349bb8 100644
--- a/src/openms/source/FILTERING/CALIBRATION/PrecursorCorrection.cpp
+++ b/src/openms/source/FILTERING/CALIBRATION/PrecursorCorrection.cpp
@@ -269,8 +269,10 @@ namespace OpenMS
         for (Size f = 0; f != features.size(); ++f)
         {
           // feature  is incompatible if believe_charge is set and charges don't match
-          if (believe_charge && features[f].getCharge() != pc_charge) continue;
-
+          if (believe_charge && features[f].getCharge() != pc_charge)
+          {
+            continue;
+          }
           // check if precursor/MS2 position overlap with feature
           if (overlaps_(features[f], rt, pc_mz, rt_tolerance_s))
           {
diff --git a/src/openms/source/FILTERING/CALIBRATION/TOFCalibration.cpp b/src/openms/source/FILTERING/CALIBRATION/TOFCalibration.cpp
index 6018dc43c15..1ca1edc429a 100644
--- a/src/openms/source/FILTERING/CALIBRATION/TOFCalibration.cpp
+++ b/src/openms/source/FILTERING/CALIBRATION/TOFCalibration.cpp
@@ -213,20 +213,20 @@ namespace OpenMS
 
     
     // iterate through all spectra
-    for (spec_iter = calib_peaks.begin(); spec_iter != calib_peaks.end(); ++spec_iter)
+    for (MSSpectrum& spec_iter : calib_peaks)
     {
-      peak_iter = spec_iter->begin();
+      peak_iter = spec_iter.begin();
       help_iter = peak_iter;
       std::vector<unsigned int> vec;
       // go through current scan
-      while (peak_iter < spec_iter->end())
+      while (peak_iter < spec_iter.end())
       {
-        while (peak_iter + 1 < spec_iter->end() && ((peak_iter + 1)->getMZ() - peak_iter->getMZ() < 1.2))
+        while (peak_iter + 1 < spec_iter.end() && ((peak_iter + 1)->getMZ() - peak_iter->getMZ() < 1.2))
         {
           ++peak_iter;
         }
 
-        vec.push_back(distance(spec_iter->begin(), help_iter));
+        vec.push_back(distance(spec_iter.begin(), help_iter));
 
         help_iter = peak_iter + 1;
         ++peak_iter;
@@ -263,9 +263,9 @@ namespace OpenMS
     //two point conversion
     if (ml3s_.empty())
     {
-      for (PeakMap::iterator spec_iter = calib_spectra.begin(); spec_iter != calib_spectra.end(); ++spec_iter)
+      for (MSSpectrum& spec_iter : calib_spectra)
       {
-        peak_iter = spec_iter->begin();
+        peak_iter = spec_iter.begin();
         double ml1, ml2;
         if (ml1s_.size() == 1)
         {
@@ -279,7 +279,7 @@ namespace OpenMS
         }
 
         // go through current scan
-        for (; peak_iter != spec_iter->end(); ++peak_iter)
+        for (; peak_iter != spec_iter.end(); ++peak_iter)
         {
           double time = peak_iter->getMZ();
           peak_iter->setPos(ml1 / 1E12 * (time * 1000 - ml2));
@@ -290,9 +290,9 @@ namespace OpenMS
     else
     {
       // three point conversion
-      for (PeakMap::iterator spec_iter = calib_spectra.begin(); spec_iter != calib_spectra.end(); ++spec_iter)
+      for (MSSpectrum& spec_iter : calib_spectra)
       {
-        peak_iter = spec_iter->begin();
+        peak_iter = spec_iter.begin();
         double ml1, ml2, ml3;
         if (ml1s_.size() == 1)
         {
@@ -308,7 +308,7 @@ namespace OpenMS
         }
 
         // go through current scan
-        for (; peak_iter != spec_iter->end(); ++peak_iter)
+        for (; peak_iter != spec_iter.end(); ++peak_iter)
         {
           double time = peak_iter->getMZ();
           peak_iter->setPos((-ml2 - (0.1E7 * (-5E5 + sqrt(0.25E12 - ml1 * ml2 * ml3 + ml1 * ml3 * time))) / (ml1 * ml3) + time) / ml3);
@@ -352,9 +352,13 @@ namespace OpenMS
       {
         double xi = mQ_(calib_peaks_ft_[spec][monoiso[p]].getMZ(), spec);
         if (xi > calib_masses[error_medians_.size() - 1])
+        {
           continue;
+        }
         if (xi < calib_masses[0])
+        {
           continue;
+        }
         std::cout << exp_masses[p] << "\t"
                   << Math::getPPM(xi - spline(xi), exp_masses[p])
                   << std::endl;
diff --git a/src/openms/source/FILTERING/DATAREDUCTION/DataFilters.cpp b/src/openms/source/FILTERING/DATAREDUCTION/DataFilters.cpp
index 611b4bc07ac..7e0ff32811f 100644
--- a/src/openms/source/FILTERING/DATAREDUCTION/DataFilters.cpp
+++ b/src/openms/source/FILTERING/DATAREDUCTION/DataFilters.cpp
@@ -136,7 +136,9 @@ namespace OpenMS
     tmp.split(' ', parts);
     SignedSize size = parts.size();
     if (size < 2)
+    {
       throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "invalid filter format", tmp);
+    }
     //field
     tmp = parts[0];
     tmp.toLower();
diff --git a/src/openms/source/FILTERING/DATAREDUCTION/FeatureFindingMetabo.cpp b/src/openms/source/FILTERING/DATAREDUCTION/FeatureFindingMetabo.cpp
index 96c2b0d582a..26606a69270 100644
--- a/src/openms/source/FILTERING/DATAREDUCTION/FeatureFindingMetabo.cpp
+++ b/src/openms/source/FILTERING/DATAREDUCTION/FeatureFindingMetabo.cpp
@@ -925,8 +925,10 @@ namespace OpenMS
       {
         // traces are sorted by m/z, so we can break when we leave the allowed window
         double diff_mz = std::fabs(input_mtraces[ext_idx].getCentroidMZ() - ref_trace_mz);
-        if (diff_mz > local_mz_range_) break;
-
+        if (diff_mz > local_mz_range_)
+        {
+          break;
+        }
         double diff_rt = std::fabs(input_mtraces[ext_idx].getCentroidRT() - ref_trace_rt);
         if (diff_rt <= local_rt_range_)
         {
diff --git a/src/openms/source/FILTERING/DATAREDUCTION/IsotopeDistributionCache.cpp b/src/openms/source/FILTERING/DATAREDUCTION/IsotopeDistributionCache.cpp
index 9a64498f372..48fe1a11b67 100644
--- a/src/openms/source/FILTERING/DATAREDUCTION/IsotopeDistributionCache.cpp
+++ b/src/openms/source/FILTERING/DATAREDUCTION/IsotopeDistributionCache.cpp
@@ -61,10 +61,10 @@ namespace OpenMS
       isotope_distributions_[index].trimmed_left = size_before - d.size();
       d.trimRight(intensity_percentage_optional);
 
-      for (IsotopeDistribution::Iterator it = d.begin(); it != d.end(); ++it)
+      for (Peak1D& it : d)
       {
-        isotope_distributions_[index].intensity.push_back(it->getIntensity());
-        //log_ << " - " << it->second << std::endl;
+        isotope_distributions_[index].intensity.push_back(it.getIntensity());
+        //log_ << " - " << it.second << std::endl;
       }
 
       //determine the number of optional peaks at the beginning/end
@@ -77,11 +77,17 @@ namespace OpenMS
         if (isotope_distributions_[index].intensity[i] < intensity_percentage)
         {
           if (!is_end && !is_begin)
+          {
             is_end = true;
+          }
           if (is_begin)
+          {
             ++begin;
+          }
           else if (is_end)
+          {
             ++end;
+          }
         }
         else if (is_begin)
         {
diff --git a/src/openms/source/FILTERING/DATAREDUCTION/MassTraceDetection.cpp b/src/openms/source/FILTERING/DATAREDUCTION/MassTraceDetection.cpp
index e2e8c471e2d..1c98d84447b 100644
--- a/src/openms/source/FILTERING/DATAREDUCTION/MassTraceDetection.cpp
+++ b/src/openms/source/FILTERING/DATAREDUCTION/MassTraceDetection.cpp
@@ -211,15 +211,17 @@ namespace OpenMS
       // *********************************************************** //
       //  Step 1: Detecting potential chromatographic apices
       // *********************************************************** //
-      for (PeakMap::ConstIterator it = input_exp.begin(); it != input_exp.end(); ++it)
+      for (const MSSpectrum& it : input_exp)
       {
         // check if this is a MS1 survey scan
-        if (it->getMSLevel() != 1) continue;
-
+        if (it.getMSLevel() != 1)
+        {
+          continue;
+        }
         std::vector<Size> indices_passing;
-        for (Size peak_idx = 0; peak_idx < it->size(); ++peak_idx)
+        for (Size peak_idx = 0; peak_idx < it.size(); ++peak_idx)
         {
-          double tmp_peak_int((*it)[peak_idx].getIntensity());
+          double tmp_peak_int((it)[peak_idx].getIntensity());
           if (tmp_peak_int > noise_threshold_int_)
           {
             // Assume that noise_threshold_int_ contains the noise level of the
@@ -233,7 +235,7 @@ namespace OpenMS
             ++total_peak_count;
           }
         }
-        PeakMap::SpectrumType tmp_spec(*it);
+        PeakMap::SpectrumType tmp_spec(it);
         tmp_spec.select(indices_passing);
         work_exp.addSpectrum(tmp_spec);
         spec_offsets.push_back(spec_offsets.back() + tmp_spec.size());
@@ -541,7 +543,10 @@ namespace OpenMS
           MassTrace new_trace(current_trace);
           new_trace.updateWeightedMeanRT();
           new_trace.updateWeightedMeanMZ();
-          if (!fwhms_mz.empty()) new_trace.fwhm_mz_avg = Math::median(fwhms_mz.begin(), fwhms_mz.end());
+          if (!fwhms_mz.empty())
+          {
+            new_trace.fwhm_mz_avg = Math::median(fwhms_mz.begin(), fwhms_mz.end());
+          }
           new_trace.setQuantMethod(quant_method_);
           //new_trace.setCentroidSD(ftl_sd);
           new_trace.updateWeightedMZsd();
@@ -554,7 +559,10 @@ namespace OpenMS
           this->setProgress(peaks_detected);
 
           // check if we already reached the (optional) maximum number of traces
-          if (max_traces > 0 && found_masstraces.size() == max_traces) break;
+          if (max_traces > 0 && found_masstraces.size() == max_traces)
+          {
+            break;
+          }
         }
       }