Added support for negative mode deconvolution (#723)

* Added support for negative mode deconvolution * Changed name of ExampleNewDeconvolution to include the word Template --------- Co-authored-by: trishorts <[email protected]>
smith-chem-wisc · Aug 4, 2023 · 40dc604 · 40dc604
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Showing 14 changed files with 318 additions and 41 deletions.
diff --git a/mzLib/MassSpectrometry/Deconvolution/Algorithms/ClassicDeconvolutionAlgorithm.cs b/mzLib/MassSpectrometry/Deconvolution/Algorithms/ClassicDeconvolutionAlgorithm.cs
@@ -74,9 +74,16 @@ public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrumToD
                             1.1) //if we're past a Th spacing, we're no longer looking at the closest isotope
                         {
                             //get the lower bound charge state
-                            int charge =
-                                (int)Math.Floor(1 /
-                                                deltaMass); //e.g. deltaMass = 0.4 Th, charge is now 2 (but might be 3)
+                            int charge = 0;
+                            if (deconParams.Polarity == Polarity.Negative)
+                            {
+                                charge = (int)Math.Floor(-1 / deltaMass); //e.g. deltaMass = 0.4 Th, charge is now 2 (but might be 3)
+                            }
+                            else
+                            {
+                                charge = (int)Math.Floor(1 / deltaMass); //e.g. deltaMass = 0.4 Th, charge is now 2 (but might be 3)
+                            }
+
                             if (charge >= deconParams.MinAssumedChargeState && charge <= deconParams.MaxAssumedChargeState)
                             {
                                 allPossibleChargeStates.Add(charge);

diff --git a/...ithms/ExampleNewDeconvolutionAlgorithm.cs → ...ampleNewDeconvolutionAlgorithmTemplate.cs b/...ithms/ExampleNewDeconvolutionAlgorithm.cs → ...ampleNewDeconvolutionAlgorithmTemplate.cs
@@ -9,16 +9,16 @@
 namespace MassSpectrometry
 {
     [ExcludeFromCodeCoverage]
-    public class ExampleNewDeconvolutionAlgorithm : DeconvolutionAlgorithm
+    public class ExampleNewDeconvolutionAlgorithmTemplate : DeconvolutionAlgorithm
     {
-        public ExampleNewDeconvolutionAlgorithm(DeconvolutionParameters deconParameters) : base(deconParameters)
+        public ExampleNewDeconvolutionAlgorithmTemplate(DeconvolutionParameters deconParameters) : base(deconParameters)
         {
 
         }
 
         public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, MzRange range = null)
         {
-            var deconParams = DeconvolutionParameters as ExampleNewDeconvolutionParameters ?? throw new MzLibException("Deconvolution params and algorithm do not match");
+            var deconParams = DeconvolutionParameters as ExampleNewDeconvolutionParametersTemplate ?? throw new MzLibException("Deconvolution params and algorithm do not match");
             range ??= spectrum.Range;
 
             throw new NotImplementedException();

diff --git a/mzLib/MassSpectrometry/Deconvolution/Deconvoluter.cs b/mzLib/MassSpectrometry/Deconvolution/Deconvoluter.cs
@@ -11,7 +11,7 @@ namespace MassSpectrometry
     public enum DeconvolutionType
     {
         ClassicDeconvolution,
-        AlexDeconvolution,
+        ExampleNewDeconvolutionTemplate,
     }
 
     /// <summary>
@@ -46,7 +46,7 @@ public IEnumerable<IsotopicEnvelope> Deconvolute(MsDataScan scan, MzRange rangeT
                 case DeconvolutionType.ClassicDeconvolution:
                     break;
 
-                case DeconvolutionType.AlexDeconvolution:
+                case DeconvolutionType.ExampleNewDeconvolutionTemplate:
                     break;
             }
 
@@ -69,8 +69,8 @@ private void ConstructDeconvolutionAlgorithm(DeconvolutionParameters deconParame
                     DeconvolutionAlgorithm = new ClassicDeconvolutionAlgorithm(deconParameters);
                     break;
 
-                case DeconvolutionType.AlexDeconvolution:
-                    DeconvolutionAlgorithm = new ExampleNewDeconvolutionAlgorithm(deconParameters);
+                case DeconvolutionType.ExampleNewDeconvolutionTemplate:
+                    DeconvolutionAlgorithm = new ExampleNewDeconvolutionAlgorithmTemplate(deconParameters);
                     break;
 
                 default: throw new MzLibException("DeconvolutionType not yet supported");

diff --git a/mzLib/MassSpectrometry/Deconvolution/DeconvoluterExtensions.cs b/mzLib/MassSpectrometry/Deconvolution/DeconvoluterExtensions.cs
@@ -18,7 +18,7 @@ public static class DeconvoluterExtensions
         /// </summary>
         /// <param name="deconvoluter">performs deconvolution</param>
         /// <param name="spectrum">spectrum to deconvolute</param>
-        /// <param name="range">mz range of returned peaks</param>
+        /// <param name="range">mz range of returned peaks, if null will deconvolute entire spectrum</param>
         /// <returns></returns>
         /// <exception cref="MzLibException"></exception>
         public static IEnumerable<IsotopicEnvelope> Deconvolute(this Deconvoluter deconvoluter,

diff --git a/mzLib/MassSpectrometry/Deconvolution/Parameters/ClassicDeconvolutionParameters.cs b/mzLib/MassSpectrometry/Deconvolution/Parameters/ClassicDeconvolutionParameters.cs
@@ -12,8 +12,6 @@ namespace MassSpectrometry
     /// </summary>
     public class ClassicDeconvolutionParameters : DeconvolutionParameters
     {
-        public int MinAssumedChargeState { get; set; }
-        public int MaxAssumedChargeState { get; set; }
         public double DeconvolutionTolerancePpm { get; set; }
         public double IntensityRatioLimit { get; set; }
 
@@ -25,12 +23,11 @@ public class ClassicDeconvolutionParameters : DeconvolutionParameters
         /// <param name="deconPpm"></param>
         /// <param name="intensityRatio"></param>
         /// <param name="range">Isolation range of the scan to be deconvoluted</param>
-        public ClassicDeconvolutionParameters(int minCharge, int maxCharge, double deconPpm, double intensityRatio) : base()
+        public ClassicDeconvolutionParameters(int minCharge, int maxCharge, double deconPpm, double intensityRatio, Polarity polarity = Polarity.Positive)
+            : base(minCharge, maxCharge, polarity)
         {
             IntensityRatioLimit = intensityRatio;
             DeconvolutionTolerancePpm = deconPpm;
-            MinAssumedChargeState = minCharge;
-            MaxAssumedChargeState = maxCharge;
         }
     }
 }
diff --git a/mzLib/MassSpectrometry/Deconvolution/Parameters/DeconvolutionParameters.cs b/mzLib/MassSpectrometry/Deconvolution/Parameters/DeconvolutionParameters.cs
@@ -12,12 +12,20 @@ namespace MassSpectrometry
     /// </summary>
     public abstract class DeconvolutionParameters
     {
+        public int MinAssumedChargeState { get; set; }
+        public int MaxAssumedChargeState { get; set; }
+        public Polarity Polarity { get; set; }
+
         /// <summary>
         /// Constructor should initialize all fields that are used by every deconvolution algorithm
         /// </summary>
-        public DeconvolutionParameters()
+        public DeconvolutionParameters(int minCharge, int maxCharge, Polarity polarity = Polarity.Positive)
         {
-
+            MinAssumedChargeState = minCharge;
+            MaxAssumedChargeState = maxCharge;
+            Polarity = polarity;
         }
     }
 }
+
+
diff --git a/mzLib/MassSpectrometry/Deconvolution/Parameters/ExampleNewDeconvolutionParameters.cs b/mzLib/MassSpectrometry/Deconvolution/Parameters/ExampleNewDeconvolutionParameters.cs
diff --git a/mzLib/MassSpectrometry/Deconvolution/Parameters/ExampleNewDeconvolutionParametersTemplate.cs b/mzLib/MassSpectrometry/Deconvolution/Parameters/ExampleNewDeconvolutionParametersTemplate.cs
@@ -0,0 +1,19 @@
+using System;
+using System.Collections.Generic;
+using System.Diagnostics.CodeAnalysis;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace MassSpectrometry
+{
+    [ExcludeFromCodeCoverage]
+    public class ExampleNewDeconvolutionParametersTemplate : DeconvolutionParameters
+    {
+        public ExampleNewDeconvolutionParametersTemplate(int minCharge, int maxCharge, Polarity polarity = Polarity.Positive)
+            : base(minCharge, maxCharge, polarity)
+        {
+
+        }
+    }
+}
diff --git a/mzLib/MassSpectrometry/MzSpectra/IsotopicEnvelope.cs b/mzLib/MassSpectrometry/MzSpectra/IsotopicEnvelope.cs
@@ -2,10 +2,11 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using Chemistry;
 
 namespace MassSpectrometry
 {
-    public class IsotopicEnvelope
+    public class IsotopicEnvelope : IHasMass
     {
         public readonly List<(double mz, double intensity)> Peaks;
         public double MonoisotopicMass { get; private set; }
@@ -35,7 +36,7 @@ public IsotopicEnvelope(List<(double mz, double intensity)> bestListOfPeaks, dou
 
         public double GetMostAbundantObservedIsotopicMass(List<(double mz, double intensity)> peaks, int charge)
         {
-            return peaks.MaxBy(p => p.intensity).mz * charge;
+            return peaks.MaxBy(p => p.intensity).mz * Math.Abs(charge);
         }
 
         public override string ToString()
@@ -46,7 +47,7 @@ public override string ToString()
         private double ScoreIsotopeEnvelope() //likely created by Stefan Solntsev using peptide data
         {
             return Peaks.Count >= 2 ?
-                TotalIntensity / Math.Pow(StDev, 0.13) * Math.Pow(Peaks.Count, 0.4) / Math.Pow(Charge, 0.06) :
+                TotalIntensity / Math.Pow(StDev, 0.13) * Math.Pow(Peaks.Count, 0.4) / Math.Pow(Math.Abs(Charge), 0.06) :
                 0;
         }
 

diff --git a/mzLib/Test/DataFiles/GUACUG_NegativeMode_Sliced.mzML b/mzLib/Test/DataFiles/GUACUG_NegativeMode_Sliced.mzML
diff --git a/mzLib/Test/Test.csproj b/mzLib/Test/Test.csproj
@@ -273,6 +273,9 @@
     <None Update="DataFiles\BinGenerationTest.mzML">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
+    <None Update="DataFiles\GUACUG_NegativeMode_Sliced.mzML">
+      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+    </None>
     <None Update="FileReadingTests\ExternalFileTypes\Ms1Feature_FlashDeconvOpenMs3.0.0_ms1.feature">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>

diff --git a/mzLib/Test/TestDeconvolution.cs b/mzLib/Test/TestDeconvolution.cs
@@ -191,5 +191,35 @@ public static void CheckClassicGetMostAbundantObservedIsotopicMass(string peptid
         }
 
         #endregion
+
+        [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);
+            Deconvoluter deconvoluter = new(DeconvolutionType.ClassicDeconvolution, deconParams);
+
+            List<IsotopicEnvelope> deconvolutionResults = deconvoluter.Deconvolute(scan).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();
+
+            Assert.That(tolerance.Within(expectedMonoMass, resultsWithPeakOfInterest.MonoisotopicMass));
+            Assert.That(expectedCharge, Is.EqualTo(resultsWithPeakOfInterest.Charge));
+        }
     }
 }
diff --git a/mzLib/mzLib.sln b/mzLib/mzLib.sln
@@ -121,8 +121,8 @@ Global
 		{04615EBF-20FC-437C-9CF7-47DA6260FAE3}.Debug|x64.ActiveCfg = Debug|x64
 		{04615EBF-20FC-437C-9CF7-47DA6260FAE3}.Debug|x64.Build.0 = Debug|x64
 		{04615EBF-20FC-437C-9CF7-47DA6260FAE3}.Release|x64.ActiveCfg = Release|x64
-		{04615EBF-20FC-437C-9CF7-47DA6260FAE3}.TestAndRelease|x64.ActiveCfg = Release|Any CPU
-		{04615EBF-20FC-437C-9CF7-47DA6260FAE3}.TestAndRelease|x64.Build.0 = Release|Any CPU
+		{04615EBF-20FC-437C-9CF7-47DA6260FAE3}.TestAndRelease|x64.ActiveCfg = Release|x64
+		{04615EBF-20FC-437C-9CF7-47DA6260FAE3}.TestAndRelease|x64.Build.0 = Release|x64
 		{E27A5C14-0C05-466A-91CE-ABB5151A69C4}.Debug|x64.ActiveCfg = Debug|x64
 		{E27A5C14-0C05-466A-91CE-ABB5151A69C4}.Debug|x64.Build.0 = Debug|x64
 		{E27A5C14-0C05-466A-91CE-ABB5151A69C4}.Release|x64.ActiveCfg = Release|x64

diff --git a/mzLib/mzLib.sln.DotSettings b/mzLib/mzLib.sln.DotSettings
@@ -4,5 +4,6 @@
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Deconvolute/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=deconvoluted/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Deconvoluter/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Monoisotopic/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Winsorize/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Winsorized/@EntryIndexedValue">True</s:Boolean></wpf:ResourceDictionary>