diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion10.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion10.java
index 9576cf8c74..bf4e0a0298 100644
--- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion10.java
+++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion10.java
@@ -19,16 +19,16 @@
 
 import org.apache.commons.lang3.tuple.Pair;
 import org.eclipse.chemclipse.converter.io.AbstractChromatogramReader;
+import org.eclipse.chemclipse.converter.l10n.ConverterMessages;
 import org.eclipse.chemclipse.logging.core.Logger;
 import org.eclipse.chemclipse.model.core.IChromatogramOverview;
 import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDReader;
 import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorChromatogram;
 import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.VendorChromatogram;
+import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.VendorIon;
 import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
 import org.eclipse.chemclipse.msd.model.core.IIonTransition;
-import org.eclipse.chemclipse.msd.model.core.IIonTransitionGroup;
-import org.eclipse.chemclipse.msd.model.core.IIonTransitionSettings;
-import org.eclipse.chemclipse.msd.model.core.IStandaloneMassSpectrum;
+import org.eclipse.chemclipse.msd.model.core.IRegularMassSpectrum;
 import org.eclipse.chemclipse.msd.model.core.MassSpectrumType;
 import org.eclipse.chemclipse.msd.model.implementation.IonTransition;
 import org.eclipse.chemclipse.msd.model.implementation.VendorMassSpectrum;
@@ -49,6 +49,7 @@
 import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.SampleType;
 import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.ScanType;
 import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.SoftwareType;
+import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.SpectrumDescriptionType;
 import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v10.SpectrumType;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.xml.sax.SAXException;
@@ -63,38 +64,17 @@ public class ChromatogramReaderVersion10 extends AbstractChromatogramReader impl
 	public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) throws IOException {
 
 		IVendorChromatogram chromatogram = null;
-		double[] retentionTimes = null;
-		double[] intensities = null;
-		//
 		try {
 			chromatogram = new VendorChromatogram();
 			MzMLType mzML = XmlReader10.getMzML(file);
-			RunType run = mzML.getRun();
-			for(ChromatogramType chromatogramType : run.getChromatogramList().getChromatogram()) {
-				if(chromatogramType.getId().equals("TIC")) {
-					if(chromatogramType.getCvParam().stream().anyMatch(n -> n.getAccession().equals("MS:1000235") && n.getName().equals("total ion current chromatogram"))) {
-						for(BinaryDataArrayType binaryDataArrayType : chromatogramType.getBinaryDataArrayList().getBinaryDataArray()) {
-							Pair<String, double[]> binaryData = BinaryReader10.parseBinaryData(binaryDataArrayType);
-							if(binaryData.getKey().equals("time")) {
-								retentionTimes = binaryData.getValue();
-							} else if(binaryData.getKey().equals("intensity")) {
-								intensities = binaryData.getValue();
-							}
-						}
-					}
-				}
-			}
-			XmlMassSpectrumReader.addIons(intensities, retentionTimes, chromatogram);
+			readTIC(mzML.getRun(), chromatogram);
 		} catch(JAXBException e) {
 			logger.warn(e);
 		} catch(SAXException e) {
 			logger.warn(e);
 		} catch(ParserConfigurationException e) {
 			logger.warn(e);
-		} catch(DataFormatException e) {
-			logger.warn(e);
 		}
-		//
 		return chromatogram;
 	}
 
@@ -102,118 +82,218 @@ public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) t
 	public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOException {
 
 		IVendorChromatogram chromatogram = null;
-		double[] intensities = null;
-		double[] mzs = null;
-		//
 		try {
 			chromatogram = new VendorChromatogram();
 			chromatogram.setFile(file);
-			//
 			MzMLType mzML = XmlReader10.getMzML(file);
-			for(ParamGroupType contact : mzML.getFileDescription().getContact()) {
-				for(CVParamType cvParam : contact.getCvParam()) {
-					if(chromatogram.getOperator().isEmpty()) {
-						chromatogram.setOperator(cvParam.getValue());
-					} else {
-						chromatogram.setOperator(String.join(", ", chromatogram.getOperator(), cvParam.getValue()));
-					}
-				}
+			readContact(mzML, chromatogram);
+			readSample(mzML, chromatogram);
+			readInstrument(mzML, chromatogram);
+			readEditHistory(mzML, chromatogram);
+			readSpectrum(mzML.getRun(), chromatogram, monitor);
+		} catch(ParserConfigurationException e) {
+			logger.warn(e);
+		} catch(SAXException e) {
+			logger.warn(e);
+		} catch(JAXBException e) {
+			logger.warn(e);
+		}
+		return chromatogram;
+	}
+
+	private IRegularMassSpectrum readMassSpectrum(SpectrumType spectrum) {
+
+		IRegularMassSpectrum massSpectrum = new VendorMassSpectrum();
+		for(CVParamType cvParam : spectrum.getCvParam()) {
+			if(cvParam.getAccession().equals("MS:1000127") && cvParam.getName().equals("centroid spectrum")) {
+				massSpectrum.setMassSpectrumType(MassSpectrumType.CENTROID);
+			} else if(cvParam.getAccession().equals("MS:1000128") && cvParam.getName().equals("profile spectrum")) {
+				massSpectrum.setMassSpectrumType(MassSpectrumType.PROFILE);
 			}
-			SampleListType sampleList = mzML.getSampleList();
-			if(sampleList != null) {
-				for(SampleType sample : sampleList.getSample()) {
-					chromatogram.setSampleName(sample.getName());
-				}
+			if(cvParam.getAccession().equals("MS:1000511") && cvParam.getName().equals("ms level")) {
+				short msLevel = Short.parseShort(cvParam.getValue());
+				massSpectrum.setMassSpectrometer(msLevel);
+			}
+		}
+		return massSpectrum;
+	}
+
+	private void readSpectrum(RunType run, IVendorChromatogram chromatogram, IProgressMonitor monitor) {
+
+		monitor.beginTask(ConverterMessages.readScans, run.getSpectrumList().getCount().intValue());
+		for(SpectrumType spectrum : run.getSpectrumList().getSpectrum()) {
+			ScanType scanType = spectrum.getSpectrumDescription().getScan();
+			if(scanType == null) {
+				continue;
 			}
-			for(InstrumentConfigurationType instrument : mzML.getInstrumentConfigurationList().getInstrumentConfiguration()) {
-				for(CVParamType cvParam : instrument.getCvParam()) {
-					if(cvParam.getAccession().equals("MS:1000554")) {
-						chromatogram.setInstrument(cvParam.getName());
+			IRegularMassSpectrum massSpectrum = readMassSpectrum(spectrum);
+			setRetentionTime(scanType, massSpectrum);
+			readIons(spectrum, massSpectrum, chromatogram);
+			chromatogram.addScan(massSpectrum);
+			monitor.worked(1);
+		}
+	}
+
+	private double getSelectedIon(SpectrumDescriptionType spectrumDescription) {
+
+		if(spectrumDescription.getPrecursorList() != null) {
+			for(PrecursorType precursorType : spectrumDescription.getPrecursorList().getPrecursor()) {
+				for(ParamGroupType paramGroupType : precursorType.getSelectedIonList().getSelectedIon()) {
+					for(CVParamType cvParam : paramGroupType.getCvParam()) {
+						if(cvParam.getAccession().equals("MS:1000744") && cvParam.getName().equals("selected ion m/z")) {
+							return Double.parseDouble(cvParam.getValue());
+						}
 					}
 				}
 			}
-			for(DataProcessingType dataProcessing : mzML.getDataProcessingList().getDataProcessing()) {
-				SoftwareType software = (SoftwareType)dataProcessing.getSoftwareRef();
-				for(ProcessingMethodType processingMethod : dataProcessing.getProcessingMethod()) {
-					for(CVParamType cvParam : processingMethod.getCvParam()) {
-						String operation = cvParam.getName();
-						String editor = software.getId();
-						chromatogram.getEditHistory().add(new EditInformation(operation, editor));
+		}
+		return 0;
+	}
+
+	private double getSelectedIonPeakIntensity(SpectrumDescriptionType spectrumDescription) {
+
+		if(spectrumDescription.getPrecursorList() != null) {
+			for(PrecursorType precursorType : spectrumDescription.getPrecursorList().getPrecursor()) {
+				for(ParamGroupType paramGroupType : precursorType.getSelectedIonList().getSelectedIon()) {
+					for(CVParamType cvParam : paramGroupType.getCvParam()) {
+						if(cvParam.getAccession().equals("MS:1000042") && cvParam.getName().equals("peak intensity")) {
+							return Double.parseDouble(cvParam.getValue());
+						}
 					}
 				}
 			}
-			RunType run = mzML.getRun();
-			for(SpectrumType spectrum : run.getSpectrumList().getSpectrum()) {
-				IStandaloneMassSpectrum massSpectrum = new VendorMassSpectrum();
-				for(CVParamType cvParam : spectrum.getCvParam()) {
-					if(cvParam.getAccession().equals("MS:1000127") && cvParam.getName().equals("centroid spectrum")) {
-						massSpectrum.setMassSpectrumType(MassSpectrumType.CENTROID);
-					} else if(cvParam.getAccession().equals("MS:1000128") && cvParam.getName().equals("profile spectrum")) {
-						massSpectrum.setMassSpectrumType(MassSpectrumType.PROFILE);
-					}
-					if(cvParam.getAccession().equals("MS:1000511") && cvParam.getName().equals("ms level")) {
-						short msLevel = Short.parseShort(cvParam.getValue());
-						massSpectrum.setMassSpectrometer(msLevel);
+		}
+		return 0;
+	}
+
+	private double getCollisionEnergy(SpectrumDescriptionType spectrumDescription) {
+
+		if(spectrumDescription.getPrecursorList() != null) {
+			for(PrecursorType precursorType : spectrumDescription.getPrecursorList().getPrecursor()) {
+				for(CVParamType cvParam : precursorType.getActivation().getCvParam()) {
+					if(cvParam.getAccession().equals("MS:1000045") && cvParam.getName().equals("collision energy")) {
+						return Double.parseDouble(cvParam.getValue());
 					}
 				}
-				ScanType scanType = spectrum.getSpectrumDescription().getScan();
-				if(scanType == null) {
-					continue;
+			}
+		}
+		return 0;
+	}
+
+	private void readIons(SpectrumType spectrum, IRegularMassSpectrum massSpectrum, IVendorChromatogram chromatogram) {
+
+		double[] intensities = null;
+		double[] mzs = null;
+		for(BinaryDataArrayType binaryDataArrayType : spectrum.getBinaryDataArrayList().getBinaryDataArray()) {
+			try {
+				Pair<String, double[]> binaryData = BinaryReader10.parseBinaryData(binaryDataArrayType);
+				if(binaryData.getKey().equals("m/z")) {
+					mzs = binaryData.getValue();
+				} else if(binaryData.getKey().equals("intensity")) {
+					intensities = binaryData.getValue();
 				}
-				for(CVParamType cvParam : scanType.getCvParam()) {
-					if(cvParam.getAccession().equals("MS:1000016") && cvParam.getName().equals("scan time")) {
-						int multiplicator = XmlReader10.getTimeMultiplicator(cvParam);
-						int retentionTime = Math.round(Float.parseFloat(cvParam.getValue()) * multiplicator);
-						massSpectrum.setRetentionTime(retentionTime);
-					}
+			} catch(DataFormatException e) {
+				logger.error(e);
+			}
+		}
+		SpectrumDescriptionType spectrumDescription = spectrum.getSpectrumDescription();
+		double selectedIon = getSelectedIon(spectrumDescription);
+		massSpectrum.setPrecursorIon(selectedIon);
+		massSpectrum.setPrecursorBasePeak(getSelectedIonPeakIntensity(spectrumDescription));
+		double collisionEnergy = getCollisionEnergy(spectrumDescription);
+		int ions = Math.min(mzs.length, intensities.length);
+		for(int i = 0; i < ions; i++) {
+			if(selectedIon != 0) {
+				IIonTransition ionTransition = new IonTransition(selectedIon, mzs[i], collisionEnergy, 1, 1, 0);
+				massSpectrum.addIon(new VendorIon(mzs[i], (float)intensities[i], ionTransition), false);
+				chromatogram.getIonTransitionSettings().getIonTransitions().add(ionTransition);
+			} else {
+				massSpectrum.addIon(new VendorIon(mzs[i], (float)intensities[i]), false);
+			}
+		}
+	}
+
+	private void setRetentionTime(ScanType scanType, IRegularMassSpectrum massSpectrum) {
+
+		for(CVParamType cvParam : scanType.getCvParam()) {
+			if(cvParam.getAccession().equals("MS:1000016") && cvParam.getName().equals("scan time")) {
+				int multiplicator = XmlReader10.getTimeMultiplicator(cvParam);
+				int retentionTime = Math.round(Float.parseFloat(cvParam.getValue()) * multiplicator);
+				massSpectrum.setRetentionTime(retentionTime);
+			}
+		}
+	}
+
+	private void readEditHistory(MzMLType mzML, IVendorChromatogram chromatogram) {
+
+		for(DataProcessingType dataProcessing : mzML.getDataProcessingList().getDataProcessing()) {
+			SoftwareType software = (SoftwareType)dataProcessing.getSoftwareRef();
+			for(ProcessingMethodType processingMethod : dataProcessing.getProcessingMethod()) {
+				for(CVParamType cvParam : processingMethod.getCvParam()) {
+					String operation = cvParam.getName();
+					String editor = software.getId();
+					chromatogram.getEditHistory().add(new EditInformation(operation, editor));
 				}
-				if(massSpectrum.isTandemMS()) {
-					IIonTransitionSettings ionTransitionSettings = chromatogram.getIonTransitionSettings();
-					IIonTransitionGroup ionTransitionGroup = ionTransitionSettings.get(0);
-					for(PrecursorType precursorType : spectrum.getSpectrumDescription().getPrecursorList().getPrecursor()) {
-						double selectedIon = 0;
-						double selectedIonPeakIntensity = 0;
-						for(ParamGroupType paramGroupType : precursorType.getSelectedIonList().getSelectedIon()) {
-							for(CVParamType cvParam : paramGroupType.getCvParam()) {
-								if(cvParam.getAccession().equals("MS:1000744") && cvParam.getName().equals("selected ion m/z")) {
-									selectedIon = Double.parseDouble(cvParam.getValue());
-								}
-								if(cvParam.getAccession().equals("MS:1000042") && cvParam.getName().equals("peak intensity")) {
-									selectedIonPeakIntensity = Double.parseDouble(cvParam.getValue());
-								}
-							}
-						}
-						double collisionEnergy = 0;
-						for(CVParamType cvParam : precursorType.getActivation().getCvParam()) {
-							if(cvParam.getAccession().equals("MS:1000045") && cvParam.getName().equals("collision energy")) {
-								collisionEnergy = Double.parseDouble(cvParam.getValue());
+			}
+		}
+	}
+
+	private void readTIC(RunType run, IVendorChromatogram chromatogram) {
+
+		double[] retentionTimes = null;
+		double[] intensities = null;
+		for(ChromatogramType chromatogramType : run.getChromatogramList().getChromatogram()) {
+			if(chromatogramType.getId().equals("TIC")) {
+				if(chromatogramType.getCvParam().stream().anyMatch(n -> n.getAccession().equals("MS:1000235") && n.getName().equals("total ion current chromatogram"))) {
+					for(BinaryDataArrayType binaryDataArrayType : chromatogramType.getBinaryDataArrayList().getBinaryDataArray()) {
+						try {
+							Pair<String, double[]> binaryData = BinaryReader10.parseBinaryData(binaryDataArrayType);
+							if(binaryData.getKey().equals("time")) {
+								retentionTimes = binaryData.getValue();
+							} else if(binaryData.getKey().equals("intensity")) {
+								intensities = binaryData.getValue();
 							}
+						} catch(DataFormatException e) {
+							logger.warn(e);
 						}
-						IIonTransition ionTransition = new IonTransition(selectedIon, selectedIonPeakIntensity, 0, 0, collisionEnergy, 0, 0, 0);
-						ionTransitionGroup.add(ionTransition);
 					}
 				}
-				for(BinaryDataArrayType binaryDataArrayType : spectrum.getBinaryDataArrayList().getBinaryDataArray()) {
-					Pair<String, double[]> binaryData = BinaryReader10.parseBinaryData(binaryDataArrayType);
-					if(binaryData.getKey().equals("m/z")) {
-						mzs = binaryData.getValue();
-					} else if(binaryData.getKey().equals("intensity")) {
-						intensities = binaryData.getValue();
-					}
+			}
+		}
+		XmlMassSpectrumReader.addTotalIntensities(intensities, retentionTimes, chromatogram);
+	}
+
+	private void readContact(MzMLType mzML, IVendorChromatogram chromatogram) {
+
+		for(ParamGroupType contact : mzML.getFileDescription().getContact()) {
+			for(CVParamType cvParam : contact.getCvParam()) {
+				if(chromatogram.getOperator().isEmpty()) {
+					chromatogram.setOperator(cvParam.getValue());
+				} else {
+					chromatogram.setOperator(String.join(", ", chromatogram.getOperator(), cvParam.getValue()));
+				}
+			}
+		}
+	}
+
+	private void readSample(MzMLType mzML, IVendorChromatogram chromatogram) {
+
+		SampleListType sampleList = mzML.getSampleList();
+		if(sampleList != null) {
+			for(SampleType sample : sampleList.getSample()) {
+				chromatogram.setSampleName(sample.getName());
+			}
+		}
+	}
+
+	private void readInstrument(MzMLType mzML, IVendorChromatogram chromatogram) {
+
+		for(InstrumentConfigurationType instrument : mzML.getInstrumentConfigurationList().getInstrumentConfiguration()) {
+			for(CVParamType cvParam : instrument.getCvParam()) {
+				if(cvParam.getAccession().equals("MS:1000554")) {
+					chromatogram.setInstrument(cvParam.getName());
 				}
-				XmlMassSpectrumReader.addIons(intensities, mzs, massSpectrum);
-				chromatogram.addScan(massSpectrum);
 			}
-		} catch(DataFormatException e) {
-			logger.warn(e);
-		} catch(ParserConfigurationException e) {
-			logger.warn(e);
-		} catch(SAXException e) {
-			logger.warn(e);
-		} catch(JAXBException e) {
-			logger.warn(e);
 		}
-		//
-		return chromatogram;
 	}
 }
diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion110.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion110.java
index 72fce2dc99..ef71152b1c 100644
--- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion110.java
+++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/ChromatogramReaderVersion110.java
@@ -19,15 +19,15 @@
 
 import org.apache.commons.lang3.tuple.Pair;
 import org.eclipse.chemclipse.converter.io.AbstractChromatogramReader;
+import org.eclipse.chemclipse.converter.l10n.ConverterMessages;
 import org.eclipse.chemclipse.logging.core.Logger;
 import org.eclipse.chemclipse.model.core.IChromatogramOverview;
 import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDReader;
 import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorChromatogram;
 import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.VendorChromatogram;
+import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.VendorIon;
 import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
 import org.eclipse.chemclipse.msd.model.core.IIonTransition;
-import org.eclipse.chemclipse.msd.model.core.IIonTransitionGroup;
-import org.eclipse.chemclipse.msd.model.core.IIonTransitionSettings;
 import org.eclipse.chemclipse.msd.model.core.IRegularMassSpectrum;
 import org.eclipse.chemclipse.msd.model.core.MassSpectrumType;
 import org.eclipse.chemclipse.msd.model.implementation.IonTransition;
@@ -43,6 +43,7 @@
 import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.PrecursorType;
 import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.RunType;
 import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.ScanType;
+import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SpectrumListType;
 import org.eclipse.chemclipse.xxd.converter.supplier.mzml.model.v110.SpectrumType;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.xml.sax.SAXException;
@@ -57,37 +58,17 @@ public class ChromatogramReaderVersion110 extends AbstractChromatogramReader imp
 	public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) throws IOException {
 
 		IVendorChromatogram chromatogram = null;
-		double[] retentionTimes = null;
-		double[] intensities = null;
-		//
 		try {
 			chromatogram = new VendorChromatogram();
 			MzMLType mzML = XmlReader110.getMzML(file);
 			MetadataReader110.readMetadata(mzML, chromatogram);
-			RunType run = mzML.getRun();
-			for(ChromatogramType chromatogramType : run.getChromatogramList().getChromatogram()) {
-				if(chromatogramType.getId().equals("TIC")) {
-					if(chromatogramType.getCvParam().stream().anyMatch(n -> n.getAccession().equals("MS:1000235") && n.getName().equals("total ion current chromatogram"))) {
-						for(BinaryDataArrayType binaryDataArrayType : chromatogramType.getBinaryDataArrayList().getBinaryDataArray()) {
-							Pair<String, double[]> binaryData = BinaryReader110.parseBinaryData(binaryDataArrayType);
-							if(binaryData.getKey().equals("time")) {
-								retentionTimes = binaryData.getValue();
-							} else if(binaryData.getKey().equals("intensity")) {
-								intensities = binaryData.getValue();
-							}
-						}
-					}
-				}
-			}
-			XmlMassSpectrumReader.addIons(intensities, retentionTimes, chromatogram);
+			readTIC(mzML.getRun(), chromatogram);
 		} catch(JAXBException e) {
 			logger.warn(e);
 		} catch(SAXException e) {
 			logger.warn(e);
 		} catch(ParserConfigurationException e) {
 			logger.warn(e);
-		} catch(DataFormatException e) {
-			logger.warn(e);
 		}
 		return chromatogram;
 	}
@@ -96,84 +77,165 @@ public IChromatogramOverview readOverview(File file, IProgressMonitor monitor) t
 	public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOException {
 
 		IVendorChromatogram chromatogram = null;
-		double[] intensities = null;
-		double[] mzs = null;
-		//
 		try {
 			chromatogram = new VendorChromatogram();
 			chromatogram.setFile(file);
-			//
 			MzMLType mzML = XmlReader110.getMzML(file);
 			MetadataReader110.readMetadata(mzML, chromatogram);
-			RunType run = mzML.getRun();
-			for(SpectrumType spectrum : run.getSpectrumList().getSpectrum()) {
-				IRegularMassSpectrum massSpectrum = new VendorMassSpectrum();
-				for(CVParamType cvParam : spectrum.getCvParam()) {
-					if(cvParam.getAccession().equals("MS:1000127") && cvParam.getName().equals("centroid spectrum")) {
-						massSpectrum.setMassSpectrumType(MassSpectrumType.CENTROID);
-					} else if(cvParam.getAccession().equals("MS:1000128") && cvParam.getName().equals("profile spectrum")) {
-						massSpectrum.setMassSpectrumType(MassSpectrumType.PROFILE);
-					}
-					if(cvParam.getAccession().equals("MS:1000511") && cvParam.getName().equals("ms level")) {
-						short msLevel = Short.parseShort(cvParam.getValue());
-						massSpectrum.setMassSpectrometer(msLevel);
+			readSpectrum(mzML.getRun(), chromatogram, monitor);
+		} catch(ParserConfigurationException e) {
+			logger.warn(e);
+		} catch(SAXException e) {
+			logger.warn(e);
+		} catch(JAXBException e) {
+			logger.warn(e);
+		}
+		return chromatogram;
+	}
+
+	private void readTIC(RunType run, IVendorChromatogram chromatogram) {
+
+		double[] retentionTimes = null;
+		double[] intensities = null;
+		for(ChromatogramType chromatogramType : run.getChromatogramList().getChromatogram()) {
+			if(chromatogramType.getId().equals("TIC")) {
+				if(chromatogramType.getCvParam().stream().anyMatch(n -> n.getAccession().equals("MS:1000235") && n.getName().equals("total ion current chromatogram"))) {
+					for(BinaryDataArrayType binaryDataArrayType : chromatogramType.getBinaryDataArrayList().getBinaryDataArray()) {
+						try {
+							Pair<String, double[]> binaryData = BinaryReader110.parseBinaryData(binaryDataArrayType);
+							if(binaryData.getKey().equals("time")) {
+								retentionTimes = binaryData.getValue();
+							} else if(binaryData.getKey().equals("intensity")) {
+								intensities = binaryData.getValue();
+							}
+						} catch(DataFormatException e) {
+							logger.warn(e);
+						}
 					}
 				}
-				for(ScanType scanType : spectrum.getScanList().getScan()) {
-					for(CVParamType cvParam : scanType.getCvParam()) {
-						if(cvParam.getAccession().equals("MS:1000016") && cvParam.getName().equals("scan start time")) {
-							float multiplicator = XmlReader110.getTimeMultiplicator(cvParam);
-							int retentionTime = Math.round(Float.parseFloat(cvParam.getValue()) * multiplicator);
-							massSpectrum.setRetentionTime(retentionTime);
+			}
+		}
+		XmlMassSpectrumReader.addTotalIntensities(intensities, retentionTimes, chromatogram);
+	}
+
+	private void readSpectrum(RunType run, IVendorChromatogram chromatogram, IProgressMonitor monitor) {
+
+		SpectrumListType spectrumList = run.getSpectrumList();
+		monitor.beginTask(ConverterMessages.readScans, spectrumList.getCount().intValue());
+		for(SpectrumType spectrum : run.getSpectrumList().getSpectrum()) {
+			IRegularMassSpectrum massSpectrum = readMassSpectrum(spectrum);
+			setRetentionTime(spectrum, massSpectrum);
+			readIons(spectrum, massSpectrum, chromatogram);
+			chromatogram.addScan(massSpectrum);
+			monitor.worked(1);
+		}
+	}
+
+	private void setRetentionTime(SpectrumType spectrum, IRegularMassSpectrum massSpectrum) {
+
+		for(ScanType scanType : spectrum.getScanList().getScan()) {
+			for(CVParamType cvParam : scanType.getCvParam()) {
+				if(cvParam.getAccession().equals("MS:1000016") && cvParam.getName().equals("scan start time")) {
+					float multiplicator = XmlReader110.getTimeMultiplicator(cvParam);
+					int retentionTime = Math.round(Float.parseFloat(cvParam.getValue()) * multiplicator);
+					massSpectrum.setRetentionTime(retentionTime);
+				}
+			}
+		}
+	}
+
+	private double getSelectedIon(SpectrumType spectrum) {
+
+		if(spectrum.getPrecursorList() != null) {
+			for(PrecursorType precursorType : spectrum.getPrecursorList().getPrecursor()) {
+				for(ParamGroupType paramGroupType : precursorType.getSelectedIonList().getSelectedIon()) {
+					for(CVParamType cvParam : paramGroupType.getCvParam()) {
+						if(cvParam.getAccession().equals("MS:1000744") && cvParam.getName().equals("selected ion m/z")) {
+							return Double.parseDouble(cvParam.getValue());
 						}
 					}
 				}
-				if(massSpectrum.isTandemMS()) {
-					IIonTransitionSettings ionTransitionSettings = chromatogram.getIonTransitionSettings();
-					IIonTransitionGroup ionTransitionGroup = ionTransitionSettings.get(0);
-					for(PrecursorType precursorType : spectrum.getPrecursorList().getPrecursor()) {
-						double selectedIon = 0;
-						double selectedIonPeakIntensity = 0;
-						for(ParamGroupType paramGroupType : precursorType.getSelectedIonList().getSelectedIon()) {
-							for(CVParamType cvParam : paramGroupType.getCvParam()) {
-								if(cvParam.getAccession().equals("MS:1000744") && cvParam.getName().equals("selected ion m/z")) {
-									selectedIon = Double.parseDouble(cvParam.getValue());
-								}
-								if(cvParam.getAccession().equals("MS:1000042") && cvParam.getName().equals("peak intensity")) {
-									selectedIonPeakIntensity = Double.parseDouble(cvParam.getValue());
-								}
-							}
-						}
-						double collisionEnergy = 0;
-						for(CVParamType cvParam : precursorType.getActivation().getCvParam()) {
-							if(cvParam.getAccession().equals("MS:1000045") && cvParam.getName().equals("collision energy")) {
-								collisionEnergy = Double.parseDouble(cvParam.getValue());
-							}
+			}
+		}
+		return 0;
+	}
+
+	private double getSelectedIonPeakIntensity(SpectrumType spectrum) {
+
+		if(spectrum.getPrecursorList() != null) {
+			for(PrecursorType precursorType : spectrum.getPrecursorList().getPrecursor()) {
+				for(ParamGroupType paramGroupType : precursorType.getSelectedIonList().getSelectedIon()) {
+					for(CVParamType cvParam : paramGroupType.getCvParam()) {
+						if(cvParam.getAccession().equals("MS:1000042") && cvParam.getName().equals("peak intensity")) {
+							return Double.parseDouble(cvParam.getValue());
 						}
-						IIonTransition ionTransition = new IonTransition(selectedIon, selectedIonPeakIntensity, 0, 0, collisionEnergy, 0, 0, 0);
-						ionTransitionGroup.add(ionTransition);
 					}
 				}
-				for(BinaryDataArrayType binaryDataArrayType : spectrum.getBinaryDataArrayList().getBinaryDataArray()) {
-					Pair<String, double[]> binaryData = BinaryReader110.parseBinaryData(binaryDataArrayType);
-					if(binaryData.getKey().equals("m/z")) {
-						mzs = binaryData.getValue();
-					} else if(binaryData.getKey().equals("intensity")) {
-						intensities = binaryData.getValue();
+			}
+		}
+		return 0;
+	}
+
+	private double getCollisionEnergy(SpectrumType spectrum) {
+
+		if(spectrum.getPrecursorList() != null) {
+			for(PrecursorType precursorType : spectrum.getPrecursorList().getPrecursor()) {
+				for(CVParamType cvParam : precursorType.getActivation().getCvParam()) {
+					if(cvParam.getAccession().equals("MS:1000045") && cvParam.getName().equals("collision energy")) {
+						return Double.parseDouble(cvParam.getValue());
 					}
 				}
-				XmlMassSpectrumReader.addIons(intensities, mzs, massSpectrum);
-				chromatogram.addScan(massSpectrum);
 			}
-		} catch(DataFormatException e) {
-			logger.warn(e);
-		} catch(ParserConfigurationException e) {
-			logger.warn(e);
-		} catch(SAXException e) {
-			logger.warn(e);
-		} catch(JAXBException e) {
-			logger.warn(e);
 		}
-		return chromatogram;
+		return 0;
+	}
+
+	private void readIons(SpectrumType spectrum, IRegularMassSpectrum massSpectrum, IVendorChromatogram chromatogram) {
+
+		double[] intensities = null;
+		double[] mzs = null;
+		for(BinaryDataArrayType binaryDataArrayType : spectrum.getBinaryDataArrayList().getBinaryDataArray()) {
+			try {
+				Pair<String, double[]> binaryData = BinaryReader110.parseBinaryData(binaryDataArrayType);
+				if(binaryData.getKey().equals("m/z")) {
+					mzs = binaryData.getValue();
+				} else if(binaryData.getKey().equals("intensity")) {
+					intensities = binaryData.getValue();
+				}
+			} catch(DataFormatException e) {
+				logger.error(e);
+			}
+		}
+		double selectedIon = getSelectedIon(spectrum);
+		massSpectrum.setPrecursorIon(selectedIon);
+		massSpectrum.setPrecursorBasePeak(getSelectedIonPeakIntensity(spectrum));
+		double collisionEnergy = getCollisionEnergy(spectrum);
+		int ions = Math.min(mzs.length, intensities.length);
+		for(int i = 0; i < ions; i++) {
+			if(selectedIon != 0) {
+				IIonTransition ionTransition = new IonTransition(selectedIon, mzs[i], collisionEnergy, 1, 1, 0);
+				massSpectrum.addIon(new VendorIon(mzs[i], (float)intensities[i], ionTransition), false);
+				chromatogram.getIonTransitionSettings().getIonTransitions().add(ionTransition);
+			} else {
+				massSpectrum.addIon(new VendorIon(mzs[i], (float)intensities[i]), false);
+			}
+		}
+	}
+
+	private IRegularMassSpectrum readMassSpectrum(SpectrumType spectrum) {
+
+		IRegularMassSpectrum massSpectrum = new VendorMassSpectrum();
+		for(CVParamType cvParam : spectrum.getCvParam()) {
+			if(cvParam.getAccession().equals("MS:1000127") && cvParam.getName().equals("centroid spectrum")) {
+				massSpectrum.setMassSpectrumType(MassSpectrumType.CENTROID);
+			} else if(cvParam.getAccession().equals("MS:1000128") && cvParam.getName().equals("profile spectrum")) {
+				massSpectrum.setMassSpectrumType(MassSpectrumType.PROFILE);
+			}
+			if(cvParam.getAccession().equals("MS:1000511") && cvParam.getName().equals("ms level")) {
+				short msLevel = Short.parseShort(cvParam.getValue());
+				massSpectrum.setMassSpectrometer(msLevel);
+			}
+		}
+		return massSpectrum;
 	}
 }
diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/XmlMassSpectrumReader.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/XmlMassSpectrumReader.java
index d2b5fada79..13d6b87f70 100644
--- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/XmlMassSpectrumReader.java
+++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/XmlMassSpectrumReader.java
@@ -23,7 +23,7 @@ private XmlMassSpectrumReader() {
 
 	}
 
-	public static void addIons(double[] intensities, double[] retentionTimes, IVendorChromatogram chromatogram) {
+	public static void addTotalIntensities(double[] intensities, double[] retentionTimes, IVendorChromatogram chromatogram) {
 
 		int tic = Math.min(retentionTimes.length, intensities.length);
 		for(int i = 0; i < tic; i++) {