Corrected some IsoDec issues. Not passing tests yet, but getting corr…

…ect charge at least.
smith-chem-wisc · Aug 6, 2024 · 1a0bd54 · 1a0bd54
2 parents 6ef4447 + 64d4a4b
commit 1a0bd54
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Showing 17 changed files with 199 additions and 145 deletions.
diff --git a/...econvolution/StandardDeconvolutionTest.cs → ...nDevelopment/StandardDeconvolutionTest.cs b/...econvolution/StandardDeconvolutionTest.cs → ...nDevelopment/StandardDeconvolutionTest.cs
diff --git a/...tCases/SinglePeakDeconvolutionTestCase.cs → ...tCases/SinglePeakDeconvolutionTestCase.cs b/...tCases/SinglePeakDeconvolutionTestCase.cs → ...tCases/SinglePeakDeconvolutionTestCase.cs
diff --git a/...ion/TestCases/TestDevelopmentTestCases.cs → ...ent/TestCases/TestDevelopmentTestCases.cs b/...ion/TestCases/TestDevelopmentTestCases.cs → ...ent/TestCases/TestDevelopmentTestCases.cs
diff --git a/...ses/WholeSpectrumDeconvolutionTestCase.cs → ...ses/WholeSpectrumDeconvolutionTestCase.cs b/...ses/WholeSpectrumDeconvolutionTestCase.cs → ...ses/WholeSpectrumDeconvolutionTestCase.cs
diff --git a/...on/TestData/Averaged_221110_CytoOnly.mzML → ...nt/TestData/Averaged_221110_CytoOnly.mzML b/...on/TestData/Averaged_221110_CytoOnly.mzML → ...nt/TestData/Averaged_221110_CytoOnly.mzML
diff --git a/...ion/TestData/Averaged_221110_HGHOnly.mzML → ...ent/TestData/Averaged_221110_HGHOnly.mzML b/...ion/TestData/Averaged_221110_HGHOnly.mzML → ...ent/TestData/Averaged_221110_HGHOnly.mzML
diff --git a/...on/TestData/Averaged_221110_UbiqOnly.mzML → ...nt/TestData/Averaged_221110_UbiqOnly.mzML b/...on/TestData/Averaged_221110_UbiqOnly.mzML → ...nt/TestData/Averaged_221110_UbiqOnly.mzML
diff --git a/mzLib/Development/Development.csproj b/mzLib/Development/Development.csproj
@@ -23,13 +23,13 @@
   </ItemGroup>
 
   <ItemGroup>
-    <None Update="Deconvolution\TestData\Averaged_221110_CytoOnly.mzML">
+    <None Update="DeconvolutionDevelopment\TestData\Averaged_221110_CytoOnly.mzML">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
-    <None Update="Deconvolution\TestData\Averaged_221110_HGHOnly.mzML">
+    <None Update="DeconvolutionDevelopment\TestData\Averaged_221110_HGHOnly.mzML">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
-    <None Update="Deconvolution\TestData\Averaged_221110_UbiqOnly.mzML">
+    <None Update="DeconvolutionDevelopment\TestData\Averaged_221110_UbiqOnly.mzML">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
   </ItemGroup>

diff --git a/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecAlgorithm.cs b/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecAlgorithm.cs
@@ -15,34 +15,10 @@ namespace MassSpectrometry
     public class IsoDecAlgorithm(DeconvolutionParameters deconParameters)
         : DeconvolutionAlgorithm(deconParameters)
     {
-        public static string _isoDecDllPath;
-        private static string _libmmDllPath;
         private static string _phaseModelPath;
-        private static string _scmlDispMdDllPath;
         static IsoDecAlgorithm()
         {
-
-            _isoDecDllPath = Path.Combine(new[]
-            {
-                AppDomain.CurrentDomain.BaseDirectory, "MassSpectrometry", "Deconvolution", "Resources", "isodeclib.dll"
-            });
-
-            _libmmDllPath = Path.Combine(new[]
-            {
-                AppDomain.CurrentDomain.BaseDirectory, "MassSpectrometry", "Deconvolution", "Resources", "libmm.dll"
-            });
-
-            _phaseModelPath = Path.Combine(new[]
-            {
-                AppDomain.CurrentDomain.BaseDirectory, "MassSpectrometry", "Deconvolution", "Resources",
-                "phase_model.bin"
-            });
-
-            _scmlDispMdDllPath = Path.Combine(new[]
-            {
-                AppDomain.CurrentDomain.BaseDirectory, "MassSpectrometry", "Deconvolution", "Resources",
-                "scml_disp_md.dll"
-            });
+            _phaseModelPath = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "Deconvolution", "Algorithms", "IsoDecResources",  "phase_model.bin");
         }
 
         [StructLayout(LayoutKind.Sequential, Pack =1)]
@@ -69,12 +45,9 @@ public struct MatchedPeak
             public int endindex;
         }
 
-
-
-        [DllImport(@"C:\Python\UniDec3\unidec\IsoDec\src\isodec\x64\Release\isodeclib.dll", CallingConvention = CallingConvention.Cdecl)]
+        [DllImport("Deconvolution/Algorithms/IsoDecResources/isodeclib.dll", CallingConvention = CallingConvention.Cdecl)]
         public static extern int process_spectrum(float[] mz, float[] intensity, int len, string modelpath, IntPtr matchedpeaks);
 
-
         public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, MzRange range)
         {
             var firstIndex = spectrum.GetClosestPeakIndex(range.Minimum);
@@ -88,7 +61,7 @@ public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, M
                 .ToArray();
 
             IntPtr matchedPeaksPtr = Marshal.AllocHGlobal(Marshal.SizeOf(typeof(MatchedPeak)) * intensities.Length);
-            int result = process_spectrum(mzs, intensities, intensities.Length, @"C:\Python\UniDec3\unidec\IsoDec\phase_model.bin", matchedPeaksPtr);
+            int result = process_spectrum(mzs, intensities, intensities.Length, _phaseModelPath , matchedPeaksPtr);
             if(result > 0)
             {
                 MatchedPeak[] matchedpeaks = new MatchedPeak[result];

diff --git a/...try/Deconvolution/Resources/isodeclib.dll → .../Algorithms/IsoDecResources/isodeclib.dll b/...try/Deconvolution/Resources/isodeclib.dll → .../Algorithms/IsoDecResources/isodeclib.dll
diff --git a/...ometry/Deconvolution/Resources/libmmd.dll → ...ion/Algorithms/IsoDecResources/libmmd.dll b/...ometry/Deconvolution/Resources/libmmd.dll → ...ion/Algorithms/IsoDecResources/libmmd.dll
diff --git a/...y/Deconvolution/Resources/phase_model.bin → ...lgorithms/IsoDecResources/phase_model.bin b/...y/Deconvolution/Resources/phase_model.bin → ...lgorithms/IsoDecResources/phase_model.bin
diff --git a/...y/Deconvolution/Resources/svml_dispmd.dll → ...lgorithms/IsoDecResources/svml_dispmd.dll b/...y/Deconvolution/Resources/svml_dispmd.dll → ...lgorithms/IsoDecResources/svml_dispmd.dll
diff --git a/mzLib/MassSpectrometry/MassSpectrometry.csproj b/mzLib/MassSpectrometry/MassSpectrometry.csproj
@@ -9,6 +9,8 @@
     <DebugType>full</DebugType>
     <DebugSymbols>true</DebugSymbols>
   </PropertyGroup>
+
+
 
   <ItemGroup>
     <PackageReference Include="CsvHelper" Version="32.0.3" />
@@ -20,19 +22,26 @@
     <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj" />
   </ItemGroup>
 
-  <ItemGroup>
-    <None Update="isodeclib.dll">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </None>
-    <None Update="Deconvolution\Resources\libmmd.dll">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </None>
-    <None Update="Deconvolution\Resources\phase_model.bin">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </None>
-    <None Update="Deconvolution\Resources\svml_dispmd.dll">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </None>
-  </ItemGroup>
+	<ItemGroup>
+		<None Remove="Deconvolution\Algorithms\isodeclib.dll" />
+		<None Remove="Deconvolution\Algorithms\libmmd.dll" />
+		<None Remove="Deconvolution\Algorithms\phase_model.bin" />
+		<None Remove="Deconvolution\Algorithms\svml_dispmd.dll" />
+	</ItemGroup>
+
+	<ItemGroup>
+		<Content Include="Deconvolution\Algorithms\IsoDecResources\isodeclib.dll">
+		  <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+		</Content>
+		<Content Include="Deconvolution\Algorithms\IsoDecResources\libmmd.dll">
+		  <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+		</Content>
+		<Content Include="Deconvolution\Algorithms\IsoDecResources\phase_model.bin">
+			<CopyToOutputDirectory>Always</CopyToOutputDirectory>
+		</Content>
+		<Content Include="Deconvolution\Algorithms\IsoDecResources\svml_dispmd.dll">
+		  <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+		</Content>
+	</ItemGroup>
 
 </Project>
diff --git a/mzLib/MassSpectrometry/isodeclib.dll b/mzLib/MassSpectrometry/isodeclib.dll
diff --git a/mzLib/Test/TestDeconvolution.cs b/mzLib/Test/TestDeconvolution.cs
@@ -64,7 +64,7 @@ public void TestDeconvolutionProteoformMultiChargeState(double selectedIonMz, in
 
             //The primary monoisotopic mass should be the same regardless of which peak in which charge state was selected for isolation.
             //this case is interesting because other monoisotopic mass may have a sodium adduct. The unit test could be expanded to consider this.
-            Assert.That(monoIsotopicMasses[0], Is.EqualTo(14037.926829).Within(.0005));
+            NUnit.Framework.Assert.That(monoIsotopicMasses[0], Is.EqualTo(14037.926829).Within(.0005));
         }
 
         [Test]
@@ -94,7 +94,7 @@ public static void CheckGetMostAbundantObservedIsotopicMass(string peptide, stri
             //check assigned correctly
             List<IsotopicEnvelope> lie2 = singlespec.Deconvolute(singleRange, minAssumedChargeState, maxAssumedChargeState, deconvolutionTolerancePpm, intensityRatioLimit).ToList();
             List<IsotopicEnvelope> lie2_charge = lie2.Where(p => p.Charge == charge).ToList();
-            Assert.That(lie2_charge[0].MostAbundantObservedIsotopicMass / charge, Is.EqualTo(m).Within(0.1));
+            NUnit.Framework.Assert.That(lie2_charge[0].MostAbundantObservedIsotopicMass / charge, Is.EqualTo(m).Within(0.1));
 
             //check that if already assigned, skips assignment and just recalls same value
             List<IsotopicEnvelope> lie3 = singlespec.Deconvolute(singleRange, minAssumedChargeState, maxAssumedChargeState, deconvolutionTolerancePpm, intensityRatioLimit).ToList();
@@ -149,8 +149,8 @@ public void TestClassicDeconvolutionProteoformMultiChargeState(double selectedIo
 
             //The primary monoisotopic mass should be the same regardless of which peak in which charge state was selected for isolation.
             //this case is interesting because other monoisotopic mass may have a sodium adduct. The unit test could be expanded to consider this.
-            Assert.That(monoIsotopicMasses[0], Is.EqualTo(14037.926829).Within(.0005));
-            Assert.That(monoIsotopicMasses2[0], Is.EqualTo(14037.926829).Within(.0005));
+            NUnit.Framework.Assert.That(monoIsotopicMasses[0], Is.EqualTo(14037.926829).Within(.0005));
+            NUnit.Framework.Assert.That(monoIsotopicMasses2[0], Is.EqualTo(14037.926829).Within(.0005));
         }
 
         [Test]
@@ -184,13 +184,42 @@ public static void CheckClassicGetMostAbundantObservedIsotopicMass(string peptid
 
             List<IsotopicEnvelope> lie2 = Deconvoluter.Deconvolute(singlespec, deconParameters, singleRange).ToList();
             List<IsotopicEnvelope> lie2_charge = lie2.Where(p => p.Charge == charge).ToList();
-            Assert.That(lie2_charge[0].MostAbundantObservedIsotopicMass / charge, Is.EqualTo(m).Within(0.1));
+            NUnit.Framework.Assert.That(lie2_charge[0].MostAbundantObservedIsotopicMass / charge, Is.EqualTo(m).Within(0.1));
 
             //check that if already assigned, skips assignment and just recalls same value
             List<IsotopicEnvelope> lie3 = Deconvoluter.Deconvolute(singlespec, deconParameters, singleRange).ToList();
             Assert.AreEqual(lie2.Select(p => p.MostAbundantObservedIsotopicMass), lie3.Select(p => p.MostAbundantObservedIsotopicMass));
         }
 
+        [Test]
+        [TestCase(373.85, -5, 1874.28)] // GUAGUC -5
+        [TestCase(467.57, -4, 1874.28)] // GUAGUC -4
+        [TestCase(623.75, -3, 1874.28)] // GUAGUC -3
+        [TestCase(936.13, -2, 1874.28)] // GUAGUC -2
+        [TestCase(473.05, -4, 1896.26)] // GUAGUC +Na -H -4
+        [TestCase(631.07, -3, 1896.26)] // GUAGUC +Na -H -3
+        [TestCase(947.121, -2, 1896.26)] // GUAGUC +Na -H -2
+        public void TestNegativeModeClassicDeconvolution(double expectedMz, int expectedCharge, double expectedMonoMass)
+        {
+            // get scan
+            string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles",
+                "GUACUG_NegativeMode_Sliced.mzML");
+            var scan = MsDataFileReader.GetDataFile(filePath).GetAllScansList().First();
+            var tolerance = new PpmTolerance(20);
+
+            // set up deconvolution
+            DeconvolutionParameters deconParams = new ClassicDeconvolutionParameters(-10, -1, 20, 3, Polarity.Negative);
+
+            List<IsotopicEnvelope> deconvolutionResults = Deconvoluter.Deconvolute(scan, deconParams).ToList();
+            // ensure each expected result is found, with correct mz, charge, and monoisotopic mass
+            var resultsWithPeakOfInterest = deconvolutionResults.FirstOrDefault(envelope =>
+                envelope.Peaks.Any(peak => tolerance.Within(peak.mz, expectedMz)));
+            if (resultsWithPeakOfInterest is null) NUnit.Framework.Assert.Fail();
+
+            NUnit.Framework.Assert.That(expectedMonoMass, Is.EqualTo(resultsWithPeakOfInterest.MonoisotopicMass).Within(0.01));
+            NUnit.Framework.Assert.That(expectedCharge, Is.EqualTo(resultsWithPeakOfInterest.Charge));
+        }
+
         #endregion
 
         #region IsoDec Deconvolution
@@ -242,8 +271,8 @@ public void TestIsoDecDeconvolutionProteoformMultiChargeState(double selectedIon
 
             //The primary monoisotopic mass should be the same regardless of which peak in which charge state was selected for isolation.
             //this case is interesting because other monoisotopic mass may have a sodium adduct. The unit test could be expanded to consider this.
-            Assert.That(monoIsotopicMasses[0], Is.EqualTo(14037.926829).Within(.0005));
-            Assert.That(monoIsotopicMasses2[0], Is.EqualTo(14037.926829).Within(.0005));
+            NUnit.Framework.Assert.That(monoIsotopicMasses[0], Is.EqualTo(14037.926829).Within(.0005));
+            NUnit.Framework.Assert.That(monoIsotopicMasses2[0], Is.EqualTo(14037.926829).Within(.0005));
         }
 
         [Test]
@@ -269,15 +298,13 @@ public static void CheckIsoDecGetMostAbundantObservedIsotopicMass(string peptide
             //check assigned correctly
             List<IsotopicEnvelope> lie2 = Deconvoluter.Deconvolute(singlespec, deconParameters, singleRange).ToList();
             List<IsotopicEnvelope> lie2_charge = lie2.Where(p => p.Charge == charge).ToList();
-            Assert.That(lie2_charge[0].MostAbundantObservedIsotopicMass / charge, Is.EqualTo(m).Within(0.1));
+            NUnit.Framework.Assert.That(lie2_charge[0].MostAbundantObservedIsotopicMass / charge, Is.EqualTo(m).Within(0.1));
 
             //check that if already assigned, skips assignment and just recalls same value
             List<IsotopicEnvelope> lie3 = Deconvoluter.Deconvolute(singlespec, deconParameters, singleRange).ToList();
             Assert.AreEqual(lie2.Select(p => p.MostAbundantObservedIsotopicMass), lie3.Select(p => p.MostAbundantObservedIsotopicMass));
         }
 
-        #endregion
-
         [Test]
         [TestCase(373.85, -5, 1874.28)] // GUAGUC -5
         [TestCase(467.57, -4, 1874.28)] // GUAGUC -4
@@ -286,7 +313,7 @@ public static void CheckIsoDecGetMostAbundantObservedIsotopicMass(string peptide
         [TestCase(473.05, -4, 1896.26)] // GUAGUC +Na -H -4
         [TestCase(631.07, -3, 1896.26)] // GUAGUC +Na -H -3
         [TestCase(947.121, -2, 1896.26)] // GUAGUC +Na -H -2
-        public void TestNegativeModeClassicDeconvolution(double expectedMz, int expectedCharge, double expectedMonoMass)
+        public void TestNegativeModeIsoDecDeconvolution(double expectedMz, int expectedCharge, double expectedMonoMass)
         {
             // get scan
             string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles",
@@ -295,18 +322,20 @@ public void TestNegativeModeClassicDeconvolution(double expectedMz, int expected
             var tolerance = new PpmTolerance(20);
 
             // set up deconvolution
-            DeconvolutionParameters deconParams = new ClassicDeconvolutionParameters(-10, -1, 20, 3, Polarity.Negative);
+            DeconvolutionParameters deconParams = new IsoDecDeconvolutionParameters(Polarity.Negative);
 
             List<IsotopicEnvelope> deconvolutionResults = Deconvoluter.Deconvolute(scan, deconParams).ToList();
             // ensure each expected result is found, with correct mz, charge, and monoisotopic mass
             var resultsWithPeakOfInterest = deconvolutionResults.FirstOrDefault(envelope =>
                 envelope.Peaks.Any(peak => tolerance.Within(peak.mz, expectedMz)));
-            if (resultsWithPeakOfInterest is null) Assert.Fail();
+            if (resultsWithPeakOfInterest is null) NUnit.Framework.Assert.Fail();
 
-            Assert.That(tolerance.Within(expectedMonoMass, resultsWithPeakOfInterest.MonoisotopicMass));
-            Assert.That(expectedCharge, Is.EqualTo(resultsWithPeakOfInterest.Charge));
+            NUnit.Framework.Assert.That(expectedMonoMass, Is.EqualTo(resultsWithPeakOfInterest.MonoisotopicMass).Within(0.01));
+            NUnit.Framework.Assert.That(expectedCharge, Is.EqualTo(resultsWithPeakOfInterest.Charge));
         }
 
+        #endregion
+
         [Test]
         public static void TestExampleNewDeconvolutionInDeconvoluter()
         {
@@ -318,14 +347,14 @@ public static void TestExampleNewDeconvolutionInDeconvoluter()
             dataFile.CloseDynamicConnection();
 
             // test switch statements in Deconvoluter
-            Assert.Throws<NotImplementedException>(() => Deconvoluter.Deconvolute(spectrum, deconParams));
-            Assert.Throws<NotImplementedException>(() => Deconvoluter.Deconvolute(scan, deconParams));
+            NUnit.Framework.Assert.Throws<NotImplementedException>(() => Deconvoluter.Deconvolute(spectrum, deconParams));
+            NUnit.Framework.Assert.Throws<NotImplementedException>(() => Deconvoluter.Deconvolute(scan, deconParams));
 
             // test default exceptions in deconvoluter
             var badEnumValue = (DeconvolutionType)Int32.MaxValue;
             deconParams.GetType().GetProperty("DeconvolutionType")!.SetValue(deconParams, badEnumValue);
-            Assert.Throws<MzLibException>(() => Deconvoluter.Deconvolute(spectrum, deconParams));
-            Assert.Throws<MzLibException>(() => Deconvoluter.Deconvolute(scan, deconParams));
+            NUnit.Framework.Assert.Throws<MzLibException>(() => Deconvoluter.Deconvolute(spectrum, deconParams));
+            NUnit.Framework.Assert.Throws<MzLibException>(() => Deconvoluter.Deconvolute(scan, deconParams));
         }
 
 
@@ -343,15 +372,15 @@ public static void Test_MsDataScan_GetIsolatedMassesAndCharges()
 
             // get isolated masses and charges on an MS1 scan. This means the isolation window is null.
             var ms1Result = precursorScan.GetIsolatedMassesAndCharges(precursorScan.MassSpectrum, deconParams).ToList();
-            Assert.That(ms1Result.Count, Is.EqualTo(0));
+            NUnit.Framework.Assert.That(ms1Result.Count, Is.EqualTo(0));
             ms1Result = precursorScan.GetIsolatedMassesAndCharges(precursorScan, deconParams).ToList();
-            Assert.That(ms1Result.Count, Is.EqualTo(0));
+            NUnit.Framework.Assert.That(ms1Result.Count, Is.EqualTo(0));
 
             // get isolated masses and charges on an MS2 scan. This should work correctly
             var ms2Result = fragmentationScan.GetIsolatedMassesAndCharges(precursorScan.MassSpectrum, deconParams).ToList();
-            Assert.That(ms2Result.Count, Is.EqualTo(1));
+            NUnit.Framework.Assert.That(ms2Result.Count, Is.EqualTo(1));
             ms2Result = fragmentationScan.GetIsolatedMassesAndCharges(precursorScan, deconParams).ToList();
-            Assert.That(ms2Result.Count, Is.EqualTo(1));
+            NUnit.Framework.Assert.That(ms2Result.Count, Is.EqualTo(1));
         }
     }
 }
diff --git a/mzLib/mzLib.nuspec b/mzLib/mzLib.nuspec
@@ -42,6 +42,10 @@
     <file src="Chemistry\bin\x64\Release\net8.0\Chemistry.dll" target="lib\net8.0" />
     <file src="FlashLFQ\bin\x64\Release\net8.0\FlashLFQ.dll" target="lib\net8.0" />
     <file src="MassSpectrometry\bin\x64\Release\net8.0\MassSpectrometry.dll" target="lib\net8.0" />
+    <file src="MassSpectrometry\bin\x64\Release\net8.0\Deconvolution\Algorithms\IsoDecResources\isodeclib.dll" target="lib\net8.0" />
+    <file src="MassSpectrometry\bin\x64\Release\net8.0\Deconvolution\Algorithms\IsoDecResources\libmmd.dll" target="lib\net8.0" />
+    <file src="MassSpectrometry\bin\x64\Release\net8.0\Deconvolution\Algorithms\IsoDecResources\svml_dispmd.dll.dll" target="lib\net8.0" />
+    <file src="MassSpectrometry\bin\x64\Release\net8.0\Deconvolution\Algorithms\IsoDecResources\phase_mode.bin" target="lib\net8.0" />
     <file src="MzIdentML\bin\x64\Release\net8.0\MzIdentML.dll" target="lib\net8.0" />
     <file src="SpectralAveraging\bin\x64\Release\net8.0\SpectralAveraging.dll" target="lib\net8.0" />
     <file src="MzLibUtil\bin\x64\Release\net8.0\MzLibUtil.dll" target="lib\net8.0" />
@@ -64,6 +68,10 @@
     <file src="Chemistry\bin\x64\Release\net8.0\Chemistry.dll" target="lib\net8.0-windows7.0" />
     <file src="FlashLFQ\bin\x64\Release\net8.0\FlashLFQ.dll" target="lib\net8.0-windows7.0" />
     <file src="MassSpectrometry\bin\x64\Release\net8.0\MassSpectrometry.dll" target="lib\net8.0-windows7.0" />
+    <file src="MassSpectrometry\bin\x64\Release\net8.0\Deconvolution\Algorithms\IsoDecResources\isodeclib.dll" target="lib\net8.0-windows7.0" />
+    <file src="MassSpectrometry\bin\x64\Release\net8.0\Deconvolution\Algorithms\IsoDecResources\libmmd.dll" target="lib\net8.0-windows7.0" />
+    <file src="MassSpectrometry\bin\x64\Release\net8.0\Deconvolution\Algorithms\IsoDecResources\svml_dispmd.dll.dll" target="lib\net8.0-windows7.0" />
+    <file src="MassSpectrometry\bin\x64\Release\net8.0\Deconvolution\Algorithms\IsoDecResources\phase_mode.bin" target="lib\net8.0-windows7.0" />
     <file src="MzIdentML\bin\x64\Release\net8.0\MzIdentML.dll" target="lib\net8.0-windows7.0" />
     <file src="SpectralAveraging\bin\x64\Release\net8.0\SpectralAveraging.dll" target="lib\net8.0-windows7.0" />
     <file src="MzLibUtil\bin\x64\Release\net8.0\MzLibUtil.dll" target="lib\net8.0-windows7.0" />