Merge pull request #1568 from Mailaender/ms-instrument-api

Propose new API for instrument type and ionization mode
eclipse · Nov 22, 2023 · 59976c5 · 59976c5
2 parents 573624f + 879ab62
commit 59976c5
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diff --git a/....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/MSPReader.java b/....supplier.amdis/src/org/eclipse/chemclipse/msd/converter/supplier/amdis/io/MSPReader.java
@@ -72,6 +72,7 @@ public class MSPReader extends AbstractMassSpectraReader implements IMassSpectra
 	private static final Pattern ionPattern = Pattern.compile("([+]?\\d+\\.?\\d*)([\t ,;:]+)([+-]?\\d+\\.?\\d*([eE][+-]?\\d+)?)");
 	private static final Pattern precursorTypePattern = Pattern.compile("(Precursor_type:)(.*)", Pattern.CASE_INSENSITIVE);
 	private static final Pattern precursorMassPattern = Pattern.compile("(PrecursorMZ:)(.*)", Pattern.CASE_INSENSITIVE);
+	private static final Pattern instrumentTypePattern = Pattern.compile("(Instrument_type:)(.*)", Pattern.CASE_INSENSITIVE);
 	private static final Pattern instrumentPattern = Pattern.compile("(Instrument:)(.*)", Pattern.CASE_INSENSITIVE);
 	private static final Pattern collisionEnergyPattern = Pattern.compile("(Collision_energy:)(.*)", Pattern.CASE_INSENSITIVE);
 	private static final Pattern exactMassPattern = Pattern.compile("(ExactMass:)(.*)", Pattern.CASE_INSENSITIVE);
@@ -255,6 +256,9 @@ private void addMassSpectrum(IMassSpectra massSpectra, String massSpectrumData,
 		String instrument = extractContentAsString(massSpectrumData, instrumentPattern, 2);
 		massSpectrum.putProperty(IRegularLibraryMassSpectrum.PROPERTY_INSTRUMENT_NAME, instrument);
 		//
+		String instrumentType = extractContentAsString(massSpectrumData, instrumentTypePattern, 2);
+		massSpectrum.putProperty(IRegularLibraryMassSpectrum.PROPERTY_INSTRUMENT_TYPE, instrumentType);
+		//
 		String ionMode = extractContentAsString(massSpectrumData, ionModePattern, 2);
 		if(ionMode.equals("POSITIVE")) {
 			massSpectrum.setPolarity(Polarity.POSITIVE);

diff --git a/...ipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IRegularLibraryMassSpectrum.java b/...ipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IRegularLibraryMassSpectrum.java
@@ -18,6 +18,8 @@ public interface IRegularLibraryMassSpectrum extends IRegularMassSpectrum, ILibr
 	public static final String PROPERTY_PRECURSOR_TYPE = "Precursor Type"; // [M+H]+, [M-H]-, ...
 	public static final String PROPERTY_COLLISION_ENERGY = "Collision Energy"; // 30
 	public static final String PROPERTY_INSTRUMENT_NAME = "Instrument Name"; // Agilent QTOF 6530
+	public static final String PROPERTY_INSTRUMENT_TYPE = "Instrument Type"; // LC-ESI-QTOF
+	public static final String PROPERTY_IONIZATION_MODE = "Ionization Mode"; // APCI
 
 	String getPrecursorType();
 

diff --git a/...emclipse/msd/converter/supplier/amdis/converter/msp/MassBankMS2ImportConverter_ITest.java b/...emclipse/msd/converter/supplier/amdis/converter/msp/MassBankMS2ImportConverter_ITest.java
@@ -54,6 +54,7 @@ public void testMassSpectrum() {
 			assertEquals("30(NCE)", regularLibraryMassSpectrum.getProperty(IRegularLibraryMassSpectrum.PROPERTY_COLLISION_ENERGY));
 			assertEquals(Polarity.POSITIVE, regularLibraryMassSpectrum.getPolarity());
 			assertEquals("[M+H]+", regularLibraryMassSpectrum.getProperty(IRegularLibraryMassSpectrum.PROPERTY_PRECURSOR_TYPE));
+			assertEquals("LC-ESI-ITFT", regularLibraryMassSpectrum.getProperty(IRegularLibraryMassSpectrum.PROPERTY_INSTRUMENT_TYPE));
 			assertEquals("Q-Exactive Orbitrap Thermo Scientific", regularLibraryMassSpectrum.getProperty(IRegularLibraryMassSpectrum.PROPERTY_INSTRUMENT_NAME));
 		}
 	}