From abbbaa7818eb44c1c6495909ab7554ab87b6cd7b Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Thu, 7 May 2026 12:33:31 -0500
Subject: [PATCH 01/26] SMPlot: Change protein: to transcript: in description

---
 .../MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs           | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
index 071e27e79..079255458 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
@@ -496,7 +496,7 @@ protected void AnnotateProperties(LibrarySpectrum librarySpectrum = null)
 
             if (MetaDrawSettings.SpectrumDescription["Protein Accession: "])
             {
-                text.Append("Protein Accession: ");
+                text.Append("Accession: ");
                 if (SpectrumMatch.Accession.Length > 10)
                 {
                     text.Append("\r\n   " + SpectrumMatch.Accession);
@@ -509,7 +509,11 @@ protected void AnnotateProperties(LibrarySpectrum librarySpectrum = null)
 
             if (SpectrumMatch.Name != null && MetaDrawSettings.SpectrumDescription["Protein: "])
             {
-                text.Append("Protein: ");
+                if (GuiGlobalParamsViewModel.Instance.IsRnaMode)
+                    text.Append("Transcript: ");
+                else
+                    text.Append("Protein: ");
+
                 text.Append(SpectrumMatch.Name);
                 text.Append("\r\n");
             }

From 3d9a505d51d0029fbfd9148204bdb21da938d052 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Thu, 7 May 2026 13:15:58 -0500
Subject: [PATCH 02/26] SMPlot: Abbreviated Ion Labels

---
 .../GUI/MetaDraw/MetaDrawSettingsWindow.xaml  |  11 +-
 .../GuiFunctions/MetaDraw/MetaDrawSettings.cs |   3 +
 .../MetaDraw/MetaDrawSettingsSnapshot.cs      |   1 +
 .../SpectrumMatch/SpectrumMatchPlot.cs        |  29 ++++-
 .../ViewModels/MetaDrawSettingsViewModel.cs   |   7 ++
 .../MetaDraw/MetaDrawSettingsAndViewsTest.cs  |   2 +
 .../Test/MetaDraw/SpectrumMatchPlotTests.cs   | 105 ++++++++++++++++++
 7 files changed, 151 insertions(+), 7 deletions(-)

diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml b/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml
index 40fe2d1a1..6c770afe2 100644
--- a/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml
+++ b/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml
@@ -6,7 +6,7 @@
         xmlns:local="clr-namespace:MetaMorpheusGUI" 
         xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
         mc:Ignorable="d"
-        Title="Graphical Settings" Width="620" SizeToContent="Height" WindowStartupLocation="CenterScreen"
+        Title="Graphical Settings" Width="640" SizeToContent="Height" WindowStartupLocation="CenterScreen"
         Height="500" MaxHeight="700"
         d:DataContext="{x:Static guiFunctions:MetaDrawSettingsViewModel.Instance}">
 
@@ -30,7 +30,7 @@
                 <!-- main settings content -->
                 <Grid >
                     <Grid.ColumnDefinitions>
-                        <ColumnDefinition Width="Auto" />
+                        <ColumnDefinition Width="*" />
                         <ColumnDefinition Width="Auto" />
                         <ColumnDefinition Width="*" />
                     </Grid.ColumnDefinitions>
@@ -99,7 +99,7 @@
                         HorizontalAlignment="Center"
                         Background="Transparent"
                         Width="2"
-                        Margin="20,0,0,0"/>
+                        Margin="5, 0"/>
 
                     <!-- right column -->
                     <ScrollViewer Grid.Column="2" HorizontalAlignment="Stretch">
@@ -146,8 +146,11 @@
                                     <CheckBox Name="SubSuperScriptedIonAnnotations"
                                               IsChecked="{Binding SubAndSuperScriptIons}"
                                               Content="Sub/superscripted ion annotations" Margin="5" />
+                                            <CheckBox Name="UseShortIonAnnotationsWhenPossible"
+                                              IsChecked="{Binding UseShortIonAnnotationsWhenPossible}"
+                                              Content="Use short ion names (bWaterLoss -> b-H2O)" Margin="5" />
 
-                                    <StackPanel Orientation="Horizontal" Margin="5 0">
+                                            <StackPanel Orientation="Horizontal" Margin="5 0">
                                         <Label Content="Annotation text size:" Width="165" />
                                         <local:IntegerTexBoxControl x:Name="TextSizeBox" Width="80" Height="24"
                                                                     Text="{Binding AnnotatedFontSize}"
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs
index 754b3a591..24f673402 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs
@@ -37,6 +37,7 @@ public static class MetaDrawSettings
         // graphic settings
         public static Dictionary<string, bool> SpectrumDescription { get; set; }
         public static bool DisplayIonAnnotations { get; set; } = true;
+        public static bool UseShortIonAnnotationsWhenPossible { get; set; } = false;
         public static bool AnnotateMzValues { get; set; } = false;
         public static bool AnnotateCharges { get; set; } = true;
         public static bool AnnotationBold { get; set; } = false;
@@ -515,6 +516,7 @@ public static MetaDrawSettingsSnapshot MakeSnapShot()
             return new MetaDrawSettingsSnapshot()
             {
                 DisplayIonAnnotations = DisplayIonAnnotations,
+                UseShortIonAnnotationsWhenPossible = UseShortIonAnnotationsWhenPossible,
                 AnnotateMzValues = AnnotateMzValues,
                 AnnotateCharges = AnnotateCharges,
                 AnnotationBold = AnnotationBold,
@@ -573,6 +575,7 @@ public static void LoadSettings(MetaDrawSettingsSnapshot settings, out bool flag
         {
             flaggedErrorOnRead = false;
             DisplayIonAnnotations = settings.DisplayIonAnnotations;
+            UseShortIonAnnotationsWhenPossible = settings.UseShortIonAnnotationsWhenPossible;
             AnnotateMzValues = settings.AnnotateMzValues;
             AnnotateCharges = settings.AnnotateCharges;
             AnnotationBold = settings.AnnotationBold;
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettingsSnapshot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettingsSnapshot.cs
index aaa34b808..9b5d3d872 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettingsSnapshot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettingsSnapshot.cs
@@ -16,6 +16,7 @@ public class MetaDrawSettingsSnapshot
         public bool AnnotationBold { get; set; } = false;
         public bool DisplayInternalIons { get; set; } = true;
         public bool DisplayInternalIonAnnotations { get; set; } = true;
+        public bool UseShortIonAnnotationsWhenPossible { get; set; } = false;
         public bool SubAndSuperScriptIons { get; set; } = true;
         public bool DrawStationarySequence { get; set; } = true;
         public bool DrawNumbersUnderStationary { get; set; } = true;
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
index 079255458..75f1e15f7 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
@@ -303,6 +303,17 @@ private void AnnotateEnvelopePeaks(MatchedFragmentIonWithEnvelope envIon, OxyCol
             }
         }
 
+
+        // Dictionary for replacing long annotation terms with shorter versions when UseShortIonAnnotationsWhenPossible is enabled
+        private static readonly Dictionary<string, string> _longToShortReplacement = new ()
+        {
+            { "WaterLoss", "-H\u2082O" },
+            { "BaseLoss", "-B" },
+            { "AmmoniaLoss", "-NH\u2083" },
+            { "Dot", "^\u2022" },
+             // Add more replacements as needed
+        };
+
         /// <summary>
         /// Builds the annotation text for a matched fragment ion
         /// </summary>
@@ -319,22 +330,25 @@ private string BuildAnnotationText(MatchedFragmentIon matchedIon, bool isBetaPep
             // Fragment Number annotation
             if (MetaDrawSettings.SubAndSuperScriptIons)
             {
+                char? previousCharacter = null;
                 foreach (var character in matchedIon.NeutralTheoreticalProduct.Annotation)
                 {
                     if (char.IsDigit(character))
                         peakAnnotationText += MetaDrawSettings.SubScriptNumbers[character - '0'];
                     else switch (character)
                     {
-                        case '-':
-                            peakAnnotationText += "\u208B";
+                        case '-' when previousCharacter is not null && char.IsNumber(previousCharacter.Value):
+                            peakAnnotationText += "\u208B"; // sub scripted Hyphen
                             break;
                         case '[':
                         case ']':
+                            previousCharacter = character;
                             continue;
                         default:
                             peakAnnotationText += character;
                             break;
                     }
+                    previousCharacter = character;
                 }
             }
             else
@@ -342,6 +356,15 @@ private string BuildAnnotationText(MatchedFragmentIon matchedIon, bool isBetaPep
                 peakAnnotationText += matchedIon.NeutralTheoreticalProduct.Annotation;
             }
 
+            if (MetaDrawSettings.UseShortIonAnnotationsWhenPossible)
+            {
+                foreach (var kvp in _longToShortReplacement.Where(kvp => peakAnnotationText.Contains(kvp.Key)))
+                {
+                    // Remove then add: bWaterLoss4 -> b4 -> b4-H20. If we simply replaced it would go bWaterLoss4 -> b-H2O4
+                    peakAnnotationText = peakAnnotationText.Replace(kvp.Key, "") + kvp.Value;
+                }
+            }
+
             // Charge annotation
             if (MetaDrawSettings.AnnotateCharges)
             {
@@ -578,7 +601,7 @@ protected void AnnotateProperties(LibrarySpectrum librarySpectrum = null)
             if (MetaDrawSettings.SpectrumDescription["Q-Value: "])
             {
                 text.Append("Q-Value: ");
-                text.Append(SpectrumMatch.QValue.ToString("F3"));
+                text.Append(SpectrumMatch.QValue.ToString("E2"));
                 text.Append("\r\n");
             }
 
diff --git a/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs b/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
index 47d63f1c6..c4a8b8853 100644
--- a/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
@@ -7,6 +7,7 @@
 using System.Threading.Tasks;
 using GuiFunctions.MetaDraw;
 using Readers;
+using System.Windows.Input;
 
 namespace GuiFunctions
 {
@@ -87,6 +88,12 @@ public ObservableCollection<CoverageTypeForTreeViewModel> CoverageColors
         public Task Initialization { get; private set; }
         public static string SettingsPath = Path.Combine(GlobalVariables.DataDir, "DefaultParameters", @"MetaDrawSettingsDefault.xml");
 
+        public bool UseShortIonAnnotationsWhenPossible
+        {
+            get => MetaDrawSettings.UseShortIonAnnotationsWhenPossible;
+            set { MetaDrawSettings.UseShortIonAnnotationsWhenPossible = value; OnPropertyChanged(nameof(UseShortIonAnnotationsWhenPossible)); }
+        }
+
         public bool ShowDecoys
         {
             get => MetaDrawSettings.ShowDecoys;
diff --git a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
index 2ec10ae3c..16c680026 100644
--- a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
+++ b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
@@ -117,6 +117,7 @@ public static void TestMetaDrawSettingsSnapshot()
             var reversedColors = MetaDrawSettings.DataVisualizationColorOrder.Reverse<OxyColor>().ToList();
             snapshot.DataVisualizationColorOrder = [..reversedColors.Select(c => c.GetColorName())];
             snapshot.BioPolymerCoverageFontSize = 3;
+            snapshot.UseShortIonAnnotationsWhenPossible = true;
 
             MetaDrawSettings.LoadSettings(snapshot, out bool flaggedError);
             Assert.That(!flaggedError);
@@ -142,6 +143,7 @@ public static void TestMetaDrawSettingsSnapshot()
             Assert.That(MetaDrawSettings.DataVisualizationColorOrder.Count, Is.EqualTo(reversedColors.Count));
             CollectionAssert.AreEqual(reversedColors.Select(c => c.GetColorName()), MetaDrawSettings.DataVisualizationColorOrder.Select(c => c.GetColorName()));
             Assert.That(snapshot.BioPolymerCoverageFontSize, Is.EqualTo(MetaDrawSettings.BioPolymerCoverageFontSize));
+            Assert.That(snapshot.UseShortIonAnnotationsWhenPossible);
 
             colorValues = MetaDrawSettings.ProductTypeToColor
                 .Select(p => $"{p.Key},{p.Value.GetColorName()}").ToList();
diff --git a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
index a0c688c40..8ffbb8a07 100644
--- a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
+++ b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
@@ -486,5 +486,110 @@ public void TestInternalFragmentWithEnvelopeDisabled()
             
             Console.WriteLine($"Total annotations: {textAnnotations.Count}, Hidden: {hiddenAnnotations.Count}");
         }
+
+        [Test]
+        public void TestUseShortIonAnnotationsWhenPossible_ReplacesLongNames()
+        {
+            MetaDrawSettings.DisplayInternalIons = true;
+            MetaDrawSettings.DisplayInternalIonAnnotations = true;
+            MetaDrawSettings.DisplayIonAnnotations = true;
+            MetaDrawSettings.AnnotateCharges = false;
+            MetaDrawSettings.AnnotateMzValues = false;
+            MetaDrawSettings.SubAndSuperScriptIons = false;
+            MetaDrawSettings.UseShortIonAnnotationsWhenPossible = true;
+
+            int originalCount = psm.MatchedIons.Count;
+            var ionToCopy = psm.MatchedIons.First();
+
+            var ionsToAdd = new List<MatchedFragmentIon>
+            {
+                CreateSyntheticNeutralLossIon(ionToCopy, ProductType.bWaterLoss),
+                CreateSyntheticNeutralLossIon(ionToCopy, ProductType.bBaseLoss),
+                CreateSyntheticNeutralLossIon(ionToCopy, ProductType.bAmmoniaLoss),
+                CreateSyntheticNeutralLossIon(ionToCopy, ProductType.zDot),
+            };
+
+            psm.MatchedIons.AddRange(ionsToAdd);
+
+            try
+            {
+                var testPlotView = new OxyPlot.Wpf.PlotView();
+                metadrawLogic.DisplaySpectrumMatch(testPlotView, psm, parentChildView, out List<string> errors);
+                Assert.That(errors == null || !errors.Any());
+
+                var annotationTexts = testPlotView.Model.Annotations
+                    .OfType<TextAnnotation>()
+                    .Select(p => p.Text)
+                    .ToList();
+
+                Assert.That(annotationTexts.Any(p => p.Contains("-H₂O")), "Expected WaterLoss replacement to -H₂O");
+                Assert.That(annotationTexts.Any(p => p.Contains("-B")), "Expected BaseLoss replacement to -B");
+                Assert.That(annotationTexts.Any(p => p.Contains("-NH₃")), "Expected AmmoniaLoss replacement to -NH₃");
+                Assert.That(annotationTexts.Any(p => p.Contains("^•")), "Expected Dot replacement to ^•");
+
+                Assert.That(annotationTexts.All(p => !p.Contains("WaterLoss")));
+                Assert.That(annotationTexts.All(p => !p.Contains("BaseLoss")));
+                Assert.That(annotationTexts.All(p => !p.Contains("AmmoniaLoss")));
+                Assert.That(annotationTexts.All(p => !p.Contains("Dot")));
+            }
+            finally
+            {
+                psm.MatchedIons.RemoveRange(originalCount, psm.MatchedIons.Count - originalCount);
+                MetaDrawSettings.UseShortIonAnnotationsWhenPossible = false;
+            }
+        }
+
+        [Test]
+        public void TestUseShortIonAnnotationsWhenPossible_WithSubAndSuperScriptIons()
+        {
+            MetaDrawSettings.DisplayInternalIons = true;
+            MetaDrawSettings.DisplayInternalIonAnnotations = true;
+            MetaDrawSettings.DisplayIonAnnotations = true;
+            MetaDrawSettings.AnnotateCharges = false;
+            MetaDrawSettings.AnnotateMzValues = false;
+            MetaDrawSettings.SubAndSuperScriptIons = true;
+            MetaDrawSettings.UseShortIonAnnotationsWhenPossible = true;
+
+            int originalCount = psm.MatchedIons.Count;
+            var ionToCopy = psm.MatchedIons.First();
+            psm.MatchedIons.Add(CreateSyntheticNeutralLossIon(ionToCopy, ProductType.bWaterLoss));
+
+            try
+            {
+                var testPlotView = new OxyPlot.Wpf.PlotView();
+                metadrawLogic.DisplaySpectrumMatch(testPlotView, psm, parentChildView, out List<string> errors);
+                Assert.That(errors == null || !errors.Any());
+
+                var annotationTexts = testPlotView.Model.Annotations
+                    .OfType<TextAnnotation>()
+                    .Select(p => p.Text)
+                    .ToList();
+
+                Assert.That(annotationTexts.Any(p => p.Contains("b₁-H₂O")), "Expected bWaterLoss to render as b₁-H₂O with sub/superscript mode");
+            }
+            finally
+            {
+                psm.MatchedIons.RemoveRange(originalCount, psm.MatchedIons.Count - originalCount);
+                MetaDrawSettings.UseShortIonAnnotationsWhenPossible = false;
+            }
+        }
+
+        private static MatchedFragmentIon CreateSyntheticNeutralLossIon(MatchedFragmentIon sourceIon, ProductType productType)
+        {
+            var sourceProduct = sourceIon.NeutralTheoreticalProduct;
+            var product = new Product(productType,
+                sourceProduct.Terminus,
+                sourceProduct.NeutralMass,
+                sourceProduct.FragmentNumber,
+                sourceProduct.ResiduePosition,
+                sourceProduct.NeutralLoss,
+                sourceProduct.SecondaryProductType,
+                sourceProduct.SecondaryFragmentNumber);
+
+            return new MatchedFragmentIon(product,
+                product.NeutralMass.ToMz(sourceIon.Charge),
+                sourceIon.Intensity,
+                sourceIon.Charge);
+        }
     }
 }

From 61032ee4381796bb72ec9b144e3281269f956d82 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Thu, 7 May 2026 13:27:49 -0500
Subject: [PATCH 03/26] Select and deselect all descriptors

---
 .../GUI/MetaDraw/MetaDrawSettingsWindow.xaml  | 40 +++++++++++------
 .../ViewModels/MetaDrawSettingsViewModel.cs   | 15 +++++++
 .../MetaDraw/MetaDrawSettingsAndViewsTest.cs  | 44 +++++++++++++++++++
 3 files changed, 86 insertions(+), 13 deletions(-)

diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml b/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml
index 6c770afe2..070a60ffa 100644
--- a/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml
+++ b/MetaMorpheus/GUI/MetaDraw/MetaDrawSettingsWindow.xaml
@@ -207,19 +207,33 @@
                                         <local:DoubleTextBoxControl x:Name ="SpectrumDescriptionFontSizeBox" Width="80" Height="24" 
                                                                     VerticalContentAlignment="Center" HorizontalContentAlignment="Center" />
                                     </StackPanel>
-                                    <ItemsControl ItemsSource="{Binding SpectrumDescriptors}">
-                                        <ItemsControl.ItemTemplate>
-                                            <DataTemplate>
-                                                <CheckBox Margin="3"
-                                                          IsChecked="{Binding IsSelected, Mode=TwoWay}"
-                                                          Content="{Binding DisplayName}">
-                                                    <CheckBox.ToolTip>
-                                                        <TextBlock Text="{Binding DisplayName, Converter={StaticResource SpectrumDescriptorToolTipConverter}}"/>
-                                                    </CheckBox.ToolTip>
-                                                </CheckBox>
-                                            </DataTemplate>
-                                        </ItemsControl.ItemTemplate>
-                                    </ItemsControl>
+                                    <Grid Margin="0 3 0 0">
+                                        <ItemsControl Grid.Column="0" ItemsSource="{Binding SpectrumDescriptors}">
+                                            <ItemsControl.ItemTemplate>
+                                                <DataTemplate>
+                                                    <CheckBox Margin="3"
+                                                              IsChecked="{Binding IsSelected, Mode=TwoWay}"
+                                                              Content="{Binding DisplayName}">
+                                                        <CheckBox.ToolTip>
+                                                            <TextBlock Text="{Binding DisplayName, Converter={StaticResource SpectrumDescriptorToolTipConverter}}"/>
+                                                        </CheckBox.ToolTip>
+                                                    </CheckBox>
+                                                </DataTemplate>
+                                            </ItemsControl.ItemTemplate>
+                                        </ItemsControl>
+
+                                        <StackPanel Grid.Column="0" HorizontalAlignment="Right" VerticalAlignment="Top">
+                                            <Button Content="Select All"
+                                                    Width="90"
+                                                    Margin="0 0 0 5"
+                                                    Command="{Binding SelectAllSpectrumDescriptorsCommand}"
+                                                    Style="{StaticResource MetaDrawButtonStyle}"/>
+                                            <Button Content="Deselect All"
+                                                    Width="90"
+                                                    Command="{Binding DeselectAllSpectrumDescriptorsCommand}"
+                                                    Style="{StaticResource MetaDrawButtonStyle}"/>
+                                        </StackPanel>
+                                    </Grid>
                                 </StackPanel>
 
                             </Expander>
diff --git a/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs b/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
index c4a8b8853..fd18da3d9 100644
--- a/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
@@ -8,6 +8,7 @@
 using GuiFunctions.MetaDraw;
 using Readers;
 using System.Windows.Input;
+using Easy.Common.Extensions;
 
 namespace GuiFunctions
 {
@@ -339,6 +340,9 @@ internal MetaDrawSettingsViewModel(bool loadAsync = true)
                 Initialization = Task.CompletedTask;
             }
 
+            SelectAllSpectrumDescriptorsCommand = new RelayCommand(SelectAllSpectrumDescriptors);
+            DeselectAllSpectrumDescriptorsCommand = new RelayCommand(DeselectAllSpectrumDescriptors);
+
             // This defaults to classic decon, and we set the charge to ensure it will work for top-down and bottom-up.
             // This is not the best approach, in the future we could try to locate the search toml when loading in a psm file and use those decon params. 
             DeconHostViewModel = new();
@@ -362,6 +366,17 @@ private async Task InitializeAsync()
             await Task.Delay(100);
         }
 
+        #endregion
+
+        #region Commands
+
+        public ICommand SelectAllSpectrumDescriptorsCommand { get; set; }
+        public ICommand DeselectAllSpectrumDescriptorsCommand { get; set; }
+
+        private void SelectAllSpectrumDescriptors() => SpectrumDescriptors.ForEach(p => p.IsSelected = true);
+        private void DeselectAllSpectrumDescriptors() => SpectrumDescriptors.ForEach(p => p.IsSelected = false);
+
+
         #endregion
 
         #region Methods
diff --git a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
index 16c680026..d01c7da5e 100644
--- a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
+++ b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
@@ -978,6 +978,50 @@ public static void TestSpectrumDescriptorViewModelSyncsWithStaticSettings()
                 Assert.That(descVm.IsSelected, Is.EqualTo(newValue));
             }
         }
+
+        [Test]
+        public static void TestSelectAllSpectrumDescriptorsCommandSelectsAll()
+        {
+            MetaDrawSettings.ResetSettings();
+            var vm = new MetaDrawSettingsViewModel(false);
+
+            for (int i = 0; i < vm.SpectrumDescriptors.Count; i++)
+            {
+                vm.SpectrumDescriptors[i].IsSelected = i % 2 == 0;
+            }
+
+            Assert.That(vm.SpectrumDescriptors.Any(p => !p.IsSelected));
+
+            vm.SelectAllSpectrumDescriptorsCommand.Execute(null);
+
+            Assert.That(vm.SpectrumDescriptors.All(p => p.IsSelected));
+            foreach (var descriptor in vm.SpectrumDescriptors)
+            {
+                Assert.That(MetaDrawSettings.SpectrumDescription[descriptor.DisplayName + ": "], Is.True);
+            }
+        }
+
+        [Test]
+        public static void TestDeselectAllSpectrumDescriptorsCommandDeselectsAll()
+        {
+            MetaDrawSettings.ResetSettings();
+            var vm = new MetaDrawSettingsViewModel(false);
+
+            for (int i = 0; i < vm.SpectrumDescriptors.Count; i++)
+            {
+                vm.SpectrumDescriptors[i].IsSelected = i % 2 == 0;
+            }
+
+            Assert.That(vm.SpectrumDescriptors.Any(p => p.IsSelected));
+
+            vm.DeselectAllSpectrumDescriptorsCommand.Execute(null);
+
+            Assert.That(vm.SpectrumDescriptors.All(p => !p.IsSelected));
+            foreach (var descriptor in vm.SpectrumDescriptors)
+            {
+                Assert.That(MetaDrawSettings.SpectrumDescription[descriptor.DisplayName + ": "], Is.False);
+            }
+        }
     }
 }
   

From 5e93055628c92ef844522b760bcf6b914a07379e Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Thu, 7 May 2026 13:48:24 -0500
Subject: [PATCH 04/26] No replotting if we are only exporting a single plot

---
 .../GuiFunctions/MetaDraw/MetaDrawLogic.cs    | 76 +++++++++++++------
 1 file changed, 52 insertions(+), 24 deletions(-)

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
index 5bed49aa1..85f3253a8 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
@@ -463,6 +463,24 @@ public MsDataScan GetMs2ScanFromPsm(SpectrumMatchFromTsv spectralMatch)
 
         #region Plot Export
 
+        private class SpectralMatchComparer : IEqualityComparer<SpectrumMatchFromTsv>
+        {
+            public static SpectralMatchComparer Instance = new();
+            public bool Equals(SpectrumMatchFromTsv x, SpectrumMatchFromTsv y)
+            {
+                if (ReferenceEquals(x, y)) return true;
+                if (x is null) return false;
+                if (y is null) return false;
+                if (x.GetType() != y.GetType()) return false;
+                return x.FullSequence == y.FullSequence && x.Ms2ScanNumber == y.Ms2ScanNumber && x.FileNameWithoutExtension == y.FileNameWithoutExtension && x.PrecursorScanNum == y.PrecursorScanNum;
+            }
+
+            public int GetHashCode(SpectrumMatchFromTsv obj)
+            {
+                return HashCode.Combine(obj.FullSequence, obj.Ms2ScanNumber, obj.FileNameWithoutExtension, obj.PrecursorScanNum);
+            }
+        }
+
         public void ExportPlot(PlotView plotView, Canvas stationaryCanvas, List<SpectrumMatchFromTsv> spectrumMatches,
             ParentChildScanPlotsView parentChildScanPlotsView, string directory, out List<string> errors,
             Canvas legendCanvas = null, Vector ptmLegendLocationVector = new(), FragmentationReanalysisViewModel? reFragment = null)
@@ -474,34 +492,44 @@ public void ExportPlot(PlotView plotView, Canvas stationaryCanvas, List<Spectrum
                 Directory.CreateDirectory(directory);
             }
 
+            // No need to recalculate the plot if we are only exporting the plot that is currently displayed. 
+            bool skipPlotRegeneration = spectrumMatches.Count == 1
+                && CurrentlyDisplayedPlots.Count == 1
+                && reFragment == null
+                && SpectralMatchComparer.Instance.Equals(CurrentlyDisplayedPlots[0].SpectrumMatch, spectrumMatches[0]);
+
             foreach (var psm in spectrumMatches)
             {
-                // get the scan
-                if (!MsDataFiles.TryGetValue(psm.FileNameWithoutExtension, out MsDataFile spectraFile))
-                {
-                    errors.Add("The spectra file could not be found for this PSM: " + psm.FileNameWithoutExtension);
-                    return;
-                }
-
-                // if we have ions that were not originally search for, cache original, find new ions, plot, replace original
                 List<MatchedFragmentIon> oldMatchedIons = null;
-                if (reFragment is not null)
-                {
-                    oldMatchedIons = psm.MatchedIons;
-                    var scan = GetMs2ScanFromPsm(psm);
-                    var newIons = reFragment.MatchIonsWithNewTypes(scan, psm, false);
-                    psm.MatchedIons = newIons;
-                }
 
-                if (plotView.Name == "plotView")
+                if (!skipPlotRegeneration)
                 {
-                    DisplaySequences(stationaryCanvas, null, null, psm);
-                    DisplaySpectrumMatch(plotView, psm, parentChildScanPlotsView, out errors);
-                }
+                    // get the scan
+                    if (!MsDataFiles.TryGetValue(psm.FileNameWithoutExtension, out MsDataFile spectraFile))
+                    {
+                        errors.Add("The spectra file could not be found for this PSM: " + psm.FileNameWithoutExtension);
+                        return;
+                    }
 
-                if (errors != null)
-                {
-                    errors.AddRange(errors);
+                    // if we have ions that were not originally search for, cache original, find new ions, plot, replace original
+                    if (reFragment is not null)
+                    {
+                        oldMatchedIons = psm.MatchedIons;
+                        var scan = GetMs2ScanFromPsm(psm);
+                        var newIons = reFragment.MatchIonsWithNewTypes(scan, psm, false);
+                        psm.MatchedIons = newIons;
+                    }
+
+                    if (plotView.Name == "plotView")
+                    {
+                        DisplaySequences(stationaryCanvas, null, null, psm);
+                        DisplaySpectrumMatch(plotView, psm, parentChildScanPlotsView, out errors);
+                    }
+
+                    if (errors != null)
+                    {
+                        errors.AddRange(errors);
+                    }
                 }
 
                 string sequence = psm.IsPeptide()
@@ -548,7 +576,7 @@ public void ExportPlot(PlotView plotView, Canvas stationaryCanvas, List<Spectrum
                     psm.MatchedIons = oldMatchedIons;
             }
 
-            if (plotView.Name == "plotView")
+            if (!skipPlotRegeneration && plotView.Name == "plotView")
             {
                 var psm = spectrumMatches.First();
 
@@ -948,4 +976,4 @@ internal static void ExportBitmap(System.Drawing.Bitmap bitmap, string path)
     }
 
     #endregion
-}
\ No newline at end of file
+}

From ff077b6536e6a870ce8ec847b069780c37c8f618 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Thu, 7 May 2026 14:07:16 -0500
Subject: [PATCH 05/26] Load Rna Mods

---
 .../ViewModels/MetaDrawSettingsViewModel.cs           | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs b/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
index fd18da3d9..274b6e818 100644
--- a/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/ViewModels/MetaDrawSettingsViewModel.cs
@@ -495,6 +495,17 @@ public void LoadPTMs()
                     theModType.Children.Add(new ModForTreeViewModel(mod.ToString(), false, mod.IdWithMotif, false, theModType));
                 }
             }
+
+            modGroups = GlobalVariables.AllRnaModsKnown.GroupBy(b => b.ModificationType);
+            foreach (var group in modGroups)
+            {
+                var theModType = new ModTypeForTreeViewModel(group.Key, false);
+                _Modifications.Add(theModType);
+                foreach (var mod in group)
+                {
+                    theModType.Children.Add(new ModForTreeViewModel(mod.ToString(), false, mod.IdWithMotif, false, theModType));
+                }
+            }
             OnPropertyChanged(nameof(Modifications));
         }
 

From a4503531adfbfb661fb21eb5a6421c424d4cfcd3 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Thu, 7 May 2026 14:07:31 -0500
Subject: [PATCH 06/26] Adjust Legend Spacing

---
 MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
index e0bbb4d16..8981a9fbc 100644
--- a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
+++ b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
@@ -319,7 +319,7 @@ private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsC
                 }
                 if (psm.Accession.Length > 10)
                     descriptionLineCount++;
-                double verticalOffset = descriptionLineCount * 1.4 * MetaDrawSettings.SpectrumDescriptionFontSize;
+                double verticalOffset = descriptionLineCount * 1.7 * MetaDrawSettings.SpectrumDescriptionFontSize;
                 
                 PtmLegend = new PtmLegendViewModel(psm, verticalOffset);
                 ChildScanPtmLegendControl.DataContext = PtmLegend;

From e6c9633cf45a939513e6337ca00ed1772ce031c2 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Thu, 7 May 2026 15:29:15 -0500
Subject: [PATCH 07/26] try catch plot generation

---
 MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs | 44 ++++++++++++++--------
 1 file changed, 28 insertions(+), 16 deletions(-)

diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
index 8981a9fbc..fc34667fa 100644
--- a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
+++ b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
@@ -305,25 +305,37 @@ private void dataGridScanNums_SelectedCellsChanged(object sender, SelectedCellsC
             double maxDisplayedPerRow = (int)Math.Round((UpperSequenceAnnotaiton.ActualWidth - 10) / MetaDrawSettings.AnnotatedSequenceTextSpacing, 0) + 7;
             MetaDrawSettings.SequenceAnnotationSegmentPerRow = (int)Math.Floor(maxDisplayedPerRow / (double)(MetaDrawSettings.SequenceAnnotaitonResiduesPerSegment + 1));
 
-            // draw the annotated spectrum
-            MetaDrawLogic.DisplaySequences(stationarySequenceCanvas, scrollableSequenceCanvas, sequenceAnnotationCanvas, psm);
-            MetaDrawLogic.DisplaySpectrumMatch(plotView, psm, itemsControlSampleViewModel, out var errors);
-
-            // add ptm legend if desired
-            if (MetaDrawSettings.ShowLegend)
+            List<string> errors = null;
+            try
             {
-                int descriptionLineCount = MetaDrawSettings.SpectrumDescription.Count(p => p.Value);
-                if (psm.Name.IsNotNullOrEmptyOrWhiteSpace())
+                // draw the annotated spectrum
+                MetaDrawLogic.DisplaySequences(stationarySequenceCanvas, scrollableSequenceCanvas,
+                    sequenceAnnotationCanvas, psm);
+                MetaDrawLogic.DisplaySpectrumMatch(plotView, psm, itemsControlSampleViewModel, out errors);
+
+                // add ptm legend if desired
+                if (MetaDrawSettings.ShowLegend)
                 {
-                    descriptionLineCount += (int)Math.Floor((psm.Name.Length - 20) / (double)SpectrumMatchPlot.MaxCharactersPerDescriptionLine);
+                    int descriptionLineCount = MetaDrawSettings.SpectrumDescription.Count(p => p.Value);
+                    if (psm.Name.IsNotNullOrEmptyOrWhiteSpace())
+                    {
+                        descriptionLineCount += (int)Math.Floor((psm.Name.Length - 20) /
+                                                                (double)SpectrumMatchPlot
+                                                                    .MaxCharactersPerDescriptionLine);
+                    }
+
+                    if (psm.Accession.Length > 10)
+                        descriptionLineCount++;
+                    double verticalOffset = descriptionLineCount * 1.7 * MetaDrawSettings.SpectrumDescriptionFontSize;
+
+                    PtmLegend = new PtmLegendViewModel(psm, verticalOffset);
+                    ChildScanPtmLegendControl.DataContext = PtmLegend;
+                    SequenceCoveragePtmLegendControl.DataContext = PtmLegend;
                 }
-                if (psm.Accession.Length > 10)
-                    descriptionLineCount++;
-                double verticalOffset = descriptionLineCount * 1.7 * MetaDrawSettings.SpectrumDescriptionFontSize;
-                
-                PtmLegend = new PtmLegendViewModel(psm, verticalOffset);
-                ChildScanPtmLegendControl.DataContext = PtmLegend;
-                SequenceCoveragePtmLegendControl.DataContext = PtmLegend;
+            }
+            catch (Exception ex)
+            {
+                MessageBox.Show("Error drawing spectrum and sequence: " + ex.Message);
             }
 
             //draw the sequence coverage if not crosslinked

From 2c423c4c3f21f69a14d4b6599b0c7d4c5def2f80 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Thu, 7 May 2026 16:55:39 -0500
Subject: [PATCH 08/26] osm mod output

---
 MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
index 85f3253a8..0e4d66549 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
@@ -532,11 +532,12 @@ public void ExportPlot(PlotView plotView, Canvas stationaryCanvas, List<Spectrum
                     }
                 }
 
-                string sequence = psm.IsPeptide()
-                    ? !(psm as PsmFromTsv).UniqueSequence.IsNullOrEmptyOrWhiteSpace()
-                        ? illegalInFileName.Replace((psm as PsmFromTsv).UniqueSequence, string.Empty)
-                        : illegalInFileName.Replace(psm.FullSequence, string.Empty)
+                var rawSequence = psm.IsPeptide()
+                    ? (!(psm as PsmFromTsv).UniqueSequence.IsNullOrEmptyOrWhiteSpace()
+                        ? (psm as PsmFromTsv).UniqueSequence
+                        : psm.FullSequence)
                     : psm.FullSequence;
+                string sequence = illegalInFileName.Replace(rawSequence, string.Empty);
 
                 if (sequence.Length > 30)
                 {

From 44d0ff651e28834cab9cb2f80b6041508fe1bd32 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Thu, 7 May 2026 18:33:11 -0500
Subject: [PATCH 09/26] Test Coverage

---
 .../GuiFunctions/MetaDraw/MetaDrawLogic.cs    | 19 +-----
 .../Util/SpectralMatchComparer.cs             | 23 +++++++
 .../GuiTests/SpectralMatchComparerTests.cs    | 65 +++++++++++++++++++
 3 files changed, 89 insertions(+), 18 deletions(-)
 create mode 100644 MetaMorpheus/GuiFunctions/Util/SpectralMatchComparer.cs
 create mode 100644 MetaMorpheus/Test/GuiTests/SpectralMatchComparerTests.cs

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
index 0e4d66549..e2a09a770 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
@@ -24,6 +24,7 @@
 using System.Runtime.CompilerServices;
 using Readers.SpectralLibrary;
 using GuiFunctions.MetaDraw;
+using GuiFunctions.Util;
 
 [assembly: InternalsVisibleTo("Test")]
 namespace GuiFunctions
@@ -463,24 +464,6 @@ public MsDataScan GetMs2ScanFromPsm(SpectrumMatchFromTsv spectralMatch)
 
         #region Plot Export
 
-        private class SpectralMatchComparer : IEqualityComparer<SpectrumMatchFromTsv>
-        {
-            public static SpectralMatchComparer Instance = new();
-            public bool Equals(SpectrumMatchFromTsv x, SpectrumMatchFromTsv y)
-            {
-                if (ReferenceEquals(x, y)) return true;
-                if (x is null) return false;
-                if (y is null) return false;
-                if (x.GetType() != y.GetType()) return false;
-                return x.FullSequence == y.FullSequence && x.Ms2ScanNumber == y.Ms2ScanNumber && x.FileNameWithoutExtension == y.FileNameWithoutExtension && x.PrecursorScanNum == y.PrecursorScanNum;
-            }
-
-            public int GetHashCode(SpectrumMatchFromTsv obj)
-            {
-                return HashCode.Combine(obj.FullSequence, obj.Ms2ScanNumber, obj.FileNameWithoutExtension, obj.PrecursorScanNum);
-            }
-        }
-
         public void ExportPlot(PlotView plotView, Canvas stationaryCanvas, List<SpectrumMatchFromTsv> spectrumMatches,
             ParentChildScanPlotsView parentChildScanPlotsView, string directory, out List<string> errors,
             Canvas legendCanvas = null, Vector ptmLegendLocationVector = new(), FragmentationReanalysisViewModel? reFragment = null)
diff --git a/MetaMorpheus/GuiFunctions/Util/SpectralMatchComparer.cs b/MetaMorpheus/GuiFunctions/Util/SpectralMatchComparer.cs
new file mode 100644
index 000000000..d096f59f2
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/Util/SpectralMatchComparer.cs
@@ -0,0 +1,23 @@
+using System;
+using System.Collections.Generic;
+using Readers;
+
+namespace GuiFunctions.Util;
+
+public class SpectralMatchComparer : IEqualityComparer<SpectrumMatchFromTsv>
+{
+    public static SpectralMatchComparer Instance = new();
+    public bool Equals(SpectrumMatchFromTsv x, SpectrumMatchFromTsv y)
+    {
+        if (ReferenceEquals(x, y)) return true;
+        if (x is null) return false;
+        if (y is null) return false;
+        if (x.GetType() != y.GetType()) return false;
+        return x.FullSequence == y.FullSequence && x.Ms2ScanNumber == y.Ms2ScanNumber && x.FileNameWithoutExtension == y.FileNameWithoutExtension && x.PrecursorScanNum == y.PrecursorScanNum;
+    }
+
+    public int GetHashCode(SpectrumMatchFromTsv obj)
+    {
+        return HashCode.Combine(obj.FullSequence, obj.Ms2ScanNumber, obj.FileNameWithoutExtension, obj.PrecursorScanNum);
+    }
+}
diff --git a/MetaMorpheus/Test/GuiTests/SpectralMatchComparerTests.cs b/MetaMorpheus/Test/GuiTests/SpectralMatchComparerTests.cs
new file mode 100644
index 000000000..2f8e66740
--- /dev/null
+++ b/MetaMorpheus/Test/GuiTests/SpectralMatchComparerTests.cs
@@ -0,0 +1,65 @@
+using System.IO;
+using GuiFunctions;
+using GuiFunctions.Util;
+using NUnit.Framework;
+using Readers;
+
+namespace Test.GuiTests;
+
+[TestFixture]
+public class SpectralMatchComparerTests
+{
+    private PsmFromTsv _psm;
+    private OsmFromTsv _osm;
+
+    [OneTimeSetUp]
+    public void OneTimeSetUp()
+    {
+        var psmPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "SequenceCoverageTestPSM.psmtsv");
+        var osmPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "Transcriptomics", "TestData", "AllOligos.osmtsv");
+
+        _psm = SpectrumMatchTsvReader.ReadTsv<PsmFromTsv>(psmPath, out _)[0];
+        _osm = SpectrumMatchTsvReader.ReadTsv<OsmFromTsv>(osmPath, out _)[0];
+    }
+
+    [Test]
+    public void Equals_ReturnsTrue_ForSameReference()
+    {
+        Assert.That(SpectralMatchComparer.Instance.Equals(_psm, _psm), Is.True);
+    }
+
+    [Test]
+    public void Equals_ReturnsFalse_WhenLeftIsNull()
+    {
+        Assert.That(SpectralMatchComparer.Instance.Equals(null, _psm), Is.False);
+    }
+
+    [Test]
+    public void Equals_ReturnsFalse_WhenRightIsNull()
+    {
+        Assert.That(SpectralMatchComparer.Instance.Equals(_psm, null), Is.False);
+    }
+
+    [Test]
+    public void Equals_ReturnsFalse_WhenTypesDiffer()
+    {
+        Assert.That(SpectralMatchComparer.Instance.Equals(_psm, _osm), Is.False);
+    }
+
+    [Test]
+    public void Equals_ReturnsTrue_WhenAllComparedFieldsMatch()
+    {
+        var psmCopy = _psm.ReplaceFullSequence(_psm.FullSequence, _psm.BaseSeq);
+
+        Assert.That(SpectralMatchComparer.Instance.Equals(_psm, psmCopy), Is.True);
+        Assert.That(SpectralMatchComparer.Instance.GetHashCode(_psm), Is.EqualTo(SpectralMatchComparer.Instance.GetHashCode(psmCopy)));
+    }
+
+    [Test]
+    public void Equals_ReturnsFalse_WhenAnyComparedFieldDiffers()
+    {
+        var psmDifferent = _psm.ReplaceFullSequence(_psm.FullSequence + "_ALT", _psm.BaseSeq);
+
+        Assert.That(SpectralMatchComparer.Instance.Equals(_psm, psmDifferent), Is.False);
+    }
+}

From c3ef46f2cf5e30f4d76b3757187879007ae6efa5 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Mon, 11 May 2026 14:09:07 -0500
Subject: [PATCH 10/26] fix test

---
 MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
index d01c7da5e..701a94db1 100644
--- a/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
+++ b/MetaMorpheus/Test/MetaDraw/MetaDrawSettingsAndViewsTest.cs
@@ -143,7 +143,7 @@ public static void TestMetaDrawSettingsSnapshot()
             Assert.That(MetaDrawSettings.DataVisualizationColorOrder.Count, Is.EqualTo(reversedColors.Count));
             CollectionAssert.AreEqual(reversedColors.Select(c => c.GetColorName()), MetaDrawSettings.DataVisualizationColorOrder.Select(c => c.GetColorName()));
             Assert.That(snapshot.BioPolymerCoverageFontSize, Is.EqualTo(MetaDrawSettings.BioPolymerCoverageFontSize));
-            Assert.That(snapshot.UseShortIonAnnotationsWhenPossible);
+            Assert.That(snapshot.UseShortIonAnnotationsWhenPossible, Is.EqualTo(MetaDrawSettings.UseShortIonAnnotationsWhenPossible));
 
             colorValues = MetaDrawSettings.ProductTypeToColor
                 .Select(p => $"{p.Key},{p.Value.GetColorName()}").ToList();

From 75bb1f69b1b39ad3fc0e00da679992f722223365 Mon Sep 17 00:00:00 2001
From: Nic Bollis <nbollis@comcast.net>
Date: Mon, 11 May 2026 13:05:02 -0500
Subject: [PATCH 11/26] MzLib 1.0.578  (#2646)

* mzlib

* Retention time prediction contract change

* revised protease and rnase custom loading

* fix tests

* more tests
---
 MetaMorpheus/CMD/CMD.csproj                   |   2 +-
 MetaMorpheus/EngineLayer/Digestion/rnases.tsv |  11 -
 MetaMorpheus/EngineLayer/EngineLayer.csproj   |   8 +-
 .../FdrAnalysis/PEPAnalysisEngine.cs          |   4 +-
 MetaMorpheus/EngineLayer/GlobalVariables.cs   | 103 +++-
 .../ProteolyticDigestion/proteases.tsv        |  23 -
 MetaMorpheus/GUI/GUI.csproj                   |   2 +-
 MetaMorpheus/GuiFunctions/GuiFunctions.csproj |   2 +-
 MetaMorpheus/MetaMorpheusSetup/Product.wxs    |  43 --
 MetaMorpheus/TaskLayer/TaskLayer.csproj       |   2 +-
 .../DatabaseTests/Task1-SearchTaskconfig.toml |   4 +-
 .../Test/DigestionModificationTests.cs        |   4 +-
 .../Test/GuiTests/LoadDigestionAgentTest.cs   | 468 ++++++++++++++++++
 MetaMorpheus/Test/MatchIonsOfAllCharges.cs    |   2 +-
 .../Test/MultiProteaseParsimonyTest.cs        |   4 +-
 MetaMorpheus/Test/Test.csproj                 |   2 +-
 MetaMorpheus/Test/TestOGlyco.cs               |  24 -
 17 files changed, 582 insertions(+), 126 deletions(-)
 delete mode 100644 MetaMorpheus/EngineLayer/Digestion/rnases.tsv
 delete mode 100644 MetaMorpheus/EngineLayer/ProteolyticDigestion/proteases.tsv
 create mode 100644 MetaMorpheus/Test/GuiTests/LoadDigestionAgentTest.cs

diff --git a/MetaMorpheus/CMD/CMD.csproj b/MetaMorpheus/CMD/CMD.csproj
index a0ff9534c..a3dc46d20 100644
--- a/MetaMorpheus/CMD/CMD.csproj
+++ b/MetaMorpheus/CMD/CMD.csproj
@@ -24,7 +24,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.577" />
+    <PackageReference Include="mzLib" Version="1.0.578" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SQLite.Interop.dll" Version="1.0.103" />
     <PackageReference Include="System.Data.SQLite" Version="1.0.118" />
diff --git a/MetaMorpheus/EngineLayer/Digestion/rnases.tsv b/MetaMorpheus/EngineLayer/Digestion/rnases.tsv
deleted file mode 100644
index 481cdc342..000000000
--- a/MetaMorpheus/EngineLayer/Digestion/rnases.tsv
+++ /dev/null
@@ -1,11 +0,0 @@
-Name	Sequences Inducing Cleavage	Sequences Preventing Cleavage	Cleavage Terminus	Cleavage Specificity	Site Regular Expression	Cleavage Mass Shifts	Notes
-RNase T1	G|			full			
-RNase T2	"G|,C|,A|,U|"			full			
-RNase A	"C|,U|"			full			
-top-down				none			
-RNase 1	"G|,C|,A|,U|"			full			
-RNase PhyM	"A|,U|"			full			
-RNase U2	"G|,A|"			full		
-Cusativin	C|			full
-RNase_MC1	"|U"			full
-colicin_E5	"G|U"			full			colicin E5 cuts after G (or Q) followed by U
diff --git a/MetaMorpheus/EngineLayer/EngineLayer.csproj b/MetaMorpheus/EngineLayer/EngineLayer.csproj
index bc253761b..8443dd761 100644
--- a/MetaMorpheus/EngineLayer/EngineLayer.csproj
+++ b/MetaMorpheus/EngineLayer/EngineLayer.csproj
@@ -29,7 +29,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.577" />
+    <PackageReference Include="mzLib" Version="1.0.578" />
     <PackageReference Include="NETStandard.Library" Version="2.0.3" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
@@ -70,9 +70,6 @@
     <None Update="Data\unimod.xml">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
-    <None Update="Digestion\rnases.tsv">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </None>
     <None Update="Glycan_Mods\NGlycan\NGlycan.gdb">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
@@ -118,9 +115,6 @@
     <None Update="Mods\Tmt.txt">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
-    <None Update="ProteolyticDigestion\proteases.tsv">
-      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
-    </None>
     <None Update="Proteomes\availableUniProtProteomes.txt.gz">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
diff --git a/MetaMorpheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs b/MetaMorpheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs
index f6c8ae180..5ef0e757b 100644
--- a/MetaMorpheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs
+++ b/MetaMorpheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs
@@ -712,7 +712,7 @@ public Dictionary<string, Dictionary<int, Tuple<double, double>>> ComputeRetenti
                         }
                         fullSequences.Add(bestMatch.SpecificBioPolymer.FullSequence);
 
-                        double predictedHydrophobicity = bestMatch.SpecificBioPolymer is PeptideWithSetModifications pep ? predictor.PredictRetentionTime(pep, out _) ?? 0 : 0;
+                        double predictedHydrophobicity = bestMatch.SpecificBioPolymer is PeptideWithSetModifications pep ? predictor.PredictRetentionTimeEquivalent(pep, out _) ?? 0 : 0;
 
                         //here i'm grouping this in 2 minute increments becuase there are cases where you get too few data points to get a good standard deviation an average. This is for stability.
                         int possibleKey = (int)(2 * Math.Round(psm.ScanRetentionTime / 2d, 0));
@@ -911,7 +911,7 @@ private static float GetRetentionTimeEquivalentZscore(SpectralMatch psm, IBioPol
                 int time = (int)(2 * Math.Round(psm.ScanRetentionTime / 2d, 0));
                 if (d[Path.GetFileName(psm.FullFilePath)].Keys.Contains(time))
                 {
-                    double predictedHydrophobicity = Peptide is PeptideWithSetModifications pep ? predictor.PredictRetentionTime(pep, out _) ?? 0 : 0;
+                    double predictedHydrophobicity = Peptide is PeptideWithSetModifications pep ? predictor.PredictRetentionTimeEquivalent(pep, out _) ?? 0 : 0;
 
                     hydrophobicityZscore = Math.Abs(d[Path.GetFileName(psm.FullFilePath)][time].Item1 - predictedHydrophobicity) / d[Path.GetFileName(psm.FullFilePath)][time].Item2;
                 }
diff --git a/MetaMorpheus/EngineLayer/GlobalVariables.cs b/MetaMorpheus/EngineLayer/GlobalVariables.cs
index f870a1c4d..bd03f3fc1 100644
--- a/MetaMorpheus/EngineLayer/GlobalVariables.cs
+++ b/MetaMorpheus/EngineLayer/GlobalVariables.cs
@@ -18,6 +18,7 @@
 using TopDownProteomics;
 using Transcriptomics.Digestion;
 using UsefulProteomicsDatabases;
+using System.Security.Cryptography;
 
 namespace EngineLayer
 {
@@ -48,6 +49,8 @@ public static class GlobalVariables
         // File locations
         public static string DataDir { get; private set; }
         public static string UserSpecifiedDataDir { get; set; }
+        public static string CustomProteasePath => Path.Combine(DataDir, "proteases_custom.tsv");
+        public static string CustomRnasePath => Path.Combine(DataDir, "rnase_custom.tsv");
 
         public static bool StopLoops { get; set; }
         public static string MetaMorpheusVersion { get; private set; }
@@ -89,6 +92,7 @@ public static void SetUpGlobalVariables()
             SetUpGlobalSettings();
             LoadDissociationTypes();
             LoadAvailableProteomes();
+            LoadDigestionAgents();
         }
 
         public static void AddMods(IEnumerable<Modification> modifications, bool modsAreFromTheTopOfProteinXml, bool isRna = false)
@@ -427,9 +431,6 @@ private static void LoadModifications()
                 }
                 // no error thrown if multiple mods with this ID are present - just pick one
             }
-            ProteaseMods = ModificationLoader.ReadModsFromFile(Path.Combine(DataDir, @"Mods", @"ProteaseMods.txt"), out var errors).ToList();
-            ProteaseDictionary.Dictionary = ProteaseDictionary.LoadProteaseDictionary(Path.Combine(DataDir, @"ProteolyticDigestion", @"proteases.tsv"), ProteaseMods);
-            RnaseDictionary.Dictionary = RnaseDictionary.LoadRnaseDictionary(Path.Combine(DataDir, @"Digestion", @"rnases.tsv"));
         }
 
         private static void LoadRnaModifications()
@@ -576,5 +577,99 @@ private static void LoadTxtGlycan()
                 _AllModsKnown.Add(glycan);
             }
         }
+
+        private static void LoadDigestionAgents()
+        {
+            if (File.Exists(CustomProteasePath))
+            {
+                try
+                {
+                    var mods = ProteaseDictionary.LoadEmbeddedProteaseMods();
+                    var result = ProteaseDictionary.LoadAndMergeCustomProteases(CustomProteasePath, mods);
+                }
+                catch (Exception e)
+                {
+                    throw new MetaMorpheusException($"Error loading custom proteases with error message: {e.Message}", e);
+                }
+            }
+            else
+            {
+                try
+                {
+                    var assembly = typeof(ProteaseDictionary).Assembly;
+
+                    // private hard-coded string path in MzLib
+                    string EmbeddedProteaseResourceName = "Proteomics.ProteolyticDigestion.proteases.tsv"; 
+
+                    var stream = assembly.GetManifestResourceStream(EmbeddedProteaseResourceName);
+                    var reader = new StreamReader(stream);
+
+                    string fileContent = reader.ReadToEnd();
+                    string[] lines = fileContent.Split(new[] { '\r', '\n' }, StringSplitOptions.RemoveEmptyEntries);
+
+                    bool foundHeader = false;
+                    using var sw = new StreamWriter(File.Create(CustomProteasePath));
+                    foreach (string line in lines) 
+                    {
+                        if (!foundHeader && !line.StartsWith("#") && line.TrimStart().StartsWith("Name\t"))
+                        {
+                            sw.WriteLine(line);
+                            foundHeader = true;
+                            break;
+                        }
+                        sw.WriteLine(line);
+                    }
+                }
+                catch (Exception e)
+                {
+                    throw new MetaMorpheusException($"Error creating default custom protease file with error message: {e.Message}", e);
+                }
+            }
+
+            if (File.Exists(CustomRnasePath))
+            {
+                try
+                {
+                    var result = RnaseDictionary.LoadAndMergeCustomRnases(CustomRnasePath);
+                }
+                catch (Exception e)
+                {
+                    throw new MetaMorpheusException($"Error loading custom rnases with error message: {e.Message}", e);
+                }
+            }
+            else
+            {
+                try
+                {
+                    var assembly = typeof(RnaseDictionary).Assembly;
+
+                    // private hard-coded string path in MzLib
+                    string EmbeddedProteaseResourceName = "Transcriptomics.Digestion.rnases.tsv";
+
+                    var stream = assembly.GetManifestResourceStream(EmbeddedProteaseResourceName);
+                    var reader = new StreamReader(stream);
+
+                    string fileContent = reader.ReadToEnd();
+                    string[] lines = fileContent.Split(new[] { '\r', '\n' }, StringSplitOptions.RemoveEmptyEntries);
+
+                    bool foundHeader = false;
+                    using var sw = new StreamWriter(File.Create(CustomRnasePath));
+                    foreach (string line in lines)
+                    {
+                        if (!foundHeader && !line.StartsWith("#") && line.TrimStart().StartsWith("Name\t"))
+                        {
+                            sw.WriteLine(line);
+                            foundHeader = true;
+                            break;
+                        }
+                        sw.WriteLine(line);
+                    }
+                }
+                catch (Exception e)
+                {
+                    throw new MetaMorpheusException($"Error creating default custom rnase file with error message: {e.Message}", e);
+                }
+            }
+        }
     }
-}
\ No newline at end of file
+}
diff --git a/MetaMorpheus/EngineLayer/ProteolyticDigestion/proteases.tsv b/MetaMorpheus/EngineLayer/ProteolyticDigestion/proteases.tsv
deleted file mode 100644
index 7bf284dda..000000000
--- a/MetaMorpheus/EngineLayer/ProteolyticDigestion/proteases.tsv
+++ /dev/null
@@ -1,23 +0,0 @@
-Name	Sequences Inducing Cleavage	Sequences Preventing Cleavage	Cleavage Terminus	Cleavage Specificity	PSI-MS Accession Number	PSI-MS Name	Site Regular Expression	Cleavage Mass Shifts	Notes
-Arg-C	R|			full	MS:1001303	Arg-C	(?<=R)(?!P)		
-Asp-N	|D			full	MS:1001304	Asp-N	(?=[BD])		
-chymotrypsin (don't cleave before proline)	"F[P]|,W[P]|,Y[P]|,L[P]|"			full	MS:1001306	Chymotrypsin	(?<=[FYWL])(?!P)		
-chymotrypsin (cleave before proline)	"F|,W|,Y|,L|"			full	MS:1001306	Chymotrypsin	(?<=[FYWL])		
-CNBr	M|			full	MS:1001307	CNBr	(?<=M)	Homoserine lactone on M
-elastase	"A|,V|,S|,G|,L|,I|"			full		Elastase	(?<=[AVSGLI])		
-Glu-C	E|			full					
-Glu-C (with asp)	"E|,D|"			full					
-Lys-C (don't cleave before proline)	K[P]|			full	MS:1001309	Lys-C	(?<=K)(?!P)		
-Lys-C (cleave before proline)	K|			full	MS:1001310	Lys-C/P	(?<=K)		
-Lys-N	|K			full					
-semi-trypsin	"K|,R|"			semi	MS:1001313	Trypsin/P	(?<=[KR])		
-trypsin	"K|,R|"			full	MS:1001313	Trypsin/P	(?<=[KR])		
-tryptophan oxidation	W|			full					
-non-specific	X|			full	MS:1001956	unspecific cleavage			
-top-down				none	MS:1001955	no cleavage						
-singleN				SingleN	MS:1001957	single cleavage			
-singleC				SingleC	MS:1001958	single cleavage			
-peptidomics				none		no cleavage			
-collagenase	GPX|GPX			full					
-StcE-trypsin	"TX|T,TX|S,SX|T,SX|S,K|,R|"			full		StcE/Trpsin			
-ProAlanase	"P|,A|"			full					
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/GUI.csproj b/MetaMorpheus/GUI/GUI.csproj
index 457bedde9..6e6d0405b 100644
--- a/MetaMorpheus/GUI/GUI.csproj
+++ b/MetaMorpheus/GUI/GUI.csproj
@@ -63,7 +63,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.577" />
+    <PackageReference Include="mzLib" Version="1.0.578" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
     <PackageReference Include="OxyPlot.Core" Version="2.0.0" />
diff --git a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj
index 5f70625ac..f3094093f 100644
--- a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj
+++ b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj
@@ -16,7 +16,7 @@
   <ItemGroup>
     <PackageReference Include="itext7" Version="8.0.5" />
     <PackageReference Include="itext7.bouncy-castle-adapter" Version="8.0.5" />
-    <PackageReference Include="mzLib" Version="1.0.577" />
+    <PackageReference Include="mzLib" Version="1.0.578" />
     <PackageReference Include="OxyPlot.Wpf" Version="2.0.0" />
     <PackageReference Include="Svg" Version="3.4.7" />
   </ItemGroup>
diff --git a/MetaMorpheus/MetaMorpheusSetup/Product.wxs b/MetaMorpheus/MetaMorpheusSetup/Product.wxs
index 90ca23627..3c523a9b9 100644
--- a/MetaMorpheus/MetaMorpheusSetup/Product.wxs
+++ b/MetaMorpheus/MetaMorpheusSetup/Product.wxs
@@ -33,8 +33,6 @@
       <ComponentGroupRef Id="Appsrc_Glycan_Mods_files" />
       <ComponentGroupRef Id="Appsrc_NGlycan_files" />
       <ComponentGroupRef Id="Appsrc_OGlycan_files" />
-      <ComponentGroupRef Id="Appsrc_ProteolyticDigestion_files" />
-      <ComponentGroupRef Id="Appsrc_Digestion_files" />
       <ComponentGroupRef Id="Appsrc_Proteomes_files" />
       <ComponentGroupRef Id="Appsrc_Contaminants_files" />
       <ComponentGroupRef Id="ExcelDefaults" />
@@ -124,12 +122,6 @@
             <Directory Id="MetaAppOGlycanFolder" Name="OGlycan" />
           </Directory>
 
-          <!--ProteolyticDigestion Folder-->
-          <Directory Id="MetaAppProteolyticDigestionFolder" Name="ProteolyticDigestion" />
-
-			<!--Digestion Folder-->
-          <Directory Id="MetaAppDigestionFolder" Name="Digestion" />
-			
           <!--Contaminants Folder-->
           <Directory Id="MetaAppContaminantsFolder" Name="Contaminants" />
 
@@ -540,13 +532,6 @@
         <File ReadOnly="no" Id="Appsrc_Mods_Mods.txt" Name="Mods.txt" Source="$(var.GUI_TargetDir)Mods\Mods.txt" />
       </Component>
 
-      <!-- ProteaseMods.txt -->
-      <Component Id="Appsrc_Mods_ProteaseMods.txt" Guid="D95A127E-AD27-49CA-91B1-B7BD55B4CFBA" Condition="OVERWRITEAPPDATA">
-        
-        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes" />
-        <File ReadOnly="no" Id="Appsrc_Mods_ProteaseMods.txt" Name="ProteaseMods.txt" Source="$(var.GUI_TargetDir)Mods\ProteaseMods.txt" />
-      </Component>
-
       <!-- substitutions.txt -->
       <Component Id="Appsrc_Mods_substitutions.txt" Guid="f108606b-f9eb-4c3c-893b-7ec33c88a1d1" Condition="OVERWRITEAPPDATA">
         
@@ -689,34 +674,6 @@
     </ComponentGroup>
   </Fragment>
 
-  <!--Builds the App ProteolyticDigestion folder-->
-  <Fragment>
-    <ComponentGroup Id="Appsrc_ProteolyticDigestion_files" Directory="MetaAppProteolyticDigestionFolder">
-      <Component Id="RemoveProteolyticDigestion" Condition="OVERWRITEAPPDATA" Guid="C0E85E53-4245-44ED-A3CB-BD5C241FC302">
-        <RemoveFolder Id="MetaAppProteolyticDigestionFolder" On="both" />
-        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes" />
-      </Component>
-      <Component Id="Appsrc_ProteolyticDigestion_proteases.tsv" Guid="A3AF0FEB-59EE-4207-9BDB-3B285D1E720E" Condition="OVERWRITEAPPDATA">
-        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes" />
-        <File ReadOnly="no" Id="Appsrc_ProteolyticDigestion_proteases.tsv" Name="proteases.tsv" Source="$(var.GUI_TargetDir)ProteolyticDigestion\proteases.tsv" />
-      </Component>
-    </ComponentGroup>
-  </Fragment>
-
-  <!--Builds the App Rnases folder-->
-  <Fragment>
-	  <ComponentGroup Id="Appsrc_Digestion_files" Directory="MetaAppDigestionFolder">
-		  <Component Id="RemoveDigestion" Condition="OVERWRITEAPPDATA" Guid="25CA934F-1A99-49D8-BB94-C52639E21615">
-			  <RemoveFolder Id="MetaAppDigestionFolder" On="both" />
-			  <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes" />
-		  </Component>
-		  <Component Id="Appsrc_Digestion_rnases.tsv" Guid="07709B54-1331-4851-92AD-26116852467C" Condition="OVERWRITEAPPDATA">
-			  <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes" />
-			  <File ReadOnly="no" Id="Appsrc_Digestion_rnases.tsv" Name="rnases.tsv" Source="$(var.GUI_TargetDir)Digestion\rnases.tsv" />
-		  </Component>
-	  </ComponentGroup>
-  </Fragment>
-
   <!--Builds the App Contaminants folder-->
   <Fragment>
     <ComponentGroup Id="Appsrc_Contaminants_files" Directory="MetaAppContaminantsFolder">
diff --git a/MetaMorpheus/TaskLayer/TaskLayer.csproj b/MetaMorpheus/TaskLayer/TaskLayer.csproj
index fb9abf18e..791a01357 100644
--- a/MetaMorpheus/TaskLayer/TaskLayer.csproj
+++ b/MetaMorpheus/TaskLayer/TaskLayer.csproj
@@ -21,7 +21,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.577" />
+    <PackageReference Include="mzLib" Version="1.0.578" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SQLite.Interop.dll" Version="1.0.103" />
diff --git a/MetaMorpheus/Test/DatabaseTests/Task1-SearchTaskconfig.toml b/MetaMorpheus/Test/DatabaseTests/Task1-SearchTaskconfig.toml
index 1e5401fc1..3fa180ade 100644
--- a/MetaMorpheus/Test/DatabaseTests/Task1-SearchTaskconfig.toml
+++ b/MetaMorpheus/Test/DatabaseTests/Task1-SearchTaskconfig.toml
@@ -88,10 +88,10 @@ MinPeptideLength = 7
 MaxPeptideLength = 50
 MaxModificationIsoforms = 1024
 MaxModsForPeptide = 2
-Protease = "chymotrypsin (don't cleave before proline)"
+Protease = "chymotrypsin|P"
 SearchModeType = "Semi"
 FragmentationTerminus = "C"
-SpecificProtease = "chymotrypsin (don't cleave before proline)"
+SpecificProtease = "chymotrypsin|P"
 GeneratehUnlabeledProteinsForSilac = true
 KeepNGlycopeptide = false
 KeepOGlycopeptide = false
diff --git a/MetaMorpheus/Test/DigestionModificationTests.cs b/MetaMorpheus/Test/DigestionModificationTests.cs
index b268440f8..22218c822 100644
--- a/MetaMorpheus/Test/DigestionModificationTests.cs
+++ b/MetaMorpheus/Test/DigestionModificationTests.cs
@@ -20,8 +20,8 @@ public static void ProteaseModTest()
             string subFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DigestionTest");
             Directory.CreateDirectory(subFolder);
 
-            string databasePath1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "ProteaseModTest.fasta");           
-            var protDic = ProteaseDictionary.LoadProteaseDictionary(Path.Combine(GlobalVariables.DataDir, @"ProteolyticDigestion", @"proteases.tsv"), GlobalVariables.ProteaseMods);
+            string databasePath1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", "ProteaseModTest.fasta");
+            var protDic = ProteaseDictionary.Dictionary;
 
             DigestionParams param = new DigestionParams(protease: "CNBr", maxMissedCleavages: 0);
             var proteinList = ProteinDbLoader.LoadProteinFasta(databasePath1, true, DecoyType.None, false, out List<string> errors);
diff --git a/MetaMorpheus/Test/GuiTests/LoadDigestionAgentTest.cs b/MetaMorpheus/Test/GuiTests/LoadDigestionAgentTest.cs
new file mode 100644
index 000000000..be9c54469
--- /dev/null
+++ b/MetaMorpheus/Test/GuiTests/LoadDigestionAgentTest.cs
@@ -0,0 +1,468 @@
+using EngineLayer;
+using MzLibUtil;
+using NUnit.Framework;
+using Proteomics.ProteolyticDigestion;
+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Reflection;
+using System.Runtime.ExceptionServices;
+using Transcriptomics.Digestion;
+
+namespace Test.GuiTests
+{
+    [TestFixture]
+    [NonParallelizable]
+    public static class LoadDigestionAgentsTest
+    {
+        private static void InvokeLoadDigestionAgents()
+        {
+            var method = typeof(GlobalVariables).GetMethod("LoadDigestionAgents", BindingFlags.NonPublic | BindingFlags.Static);
+            Assert.That(method, Is.Not.Null, "Could not find GlobalVariables.LoadDigestionAgents via reflection.");
+
+            try
+            {
+                method.Invoke(null, null);
+            }
+            catch (TargetInvocationException ex) when (ex.InnerException != null)
+            {
+                ExceptionDispatchInfo.Capture(ex.InnerException).Throw();
+            }
+        }
+
+        private static void BackupPath(string path, out string backupPath, out bool hadExistingFile, out bool hadExistingDirectory)
+        {
+            backupPath = path + ".bak";
+            hadExistingFile = File.Exists(path);
+            hadExistingDirectory = Directory.Exists(path);
+
+            if (File.Exists(backupPath))
+                File.Delete(backupPath);
+            else if (Directory.Exists(backupPath))
+                Directory.Delete(backupPath, true);
+
+            if (hadExistingFile)
+                File.Copy(path, backupPath, overwrite: true);
+            else if (hadExistingDirectory)
+                Directory.Move(path, backupPath);
+        }
+
+        private static void RestorePath(string path, string backupPath, bool hadExistingFile, bool hadExistingDirectory)
+        {
+            if (File.Exists(path))
+                File.Delete(path);
+            else if (Directory.Exists(path))
+                Directory.Delete(path, true);
+
+            if (hadExistingFile)
+                File.Copy(backupPath, path, overwrite: true);
+            else if (hadExistingDirectory)
+                Directory.Move(backupPath, path);
+
+            if (File.Exists(backupPath))
+                File.Delete(backupPath);
+            else if (Directory.Exists(backupPath))
+                Directory.Delete(backupPath, true);
+        }
+
+        private static void DeletePathIfExists(string path)
+        {
+            if (File.Exists(path))
+                File.Delete(path);
+            else if (Directory.Exists(path))
+                Directory.Delete(path, true);
+        }
+
+        private static string GetHeaderLine(string[] tsvLines)
+        {
+            // The TSV files may have comment lines starting with '#' before the header
+            return tsvLines.First(line => !line.StartsWith("#") && line.TrimStart().StartsWith("Name\t"));
+        }
+
+        private static string GetHeaderLine(Stream tsvStream)
+        {
+            var reader = new StreamReader(tsvStream);
+
+            string fileContent = reader.ReadToEnd();
+            string[] lines = fileContent.Split(new[] { '\r', '\n' }, StringSplitOptions.RemoveEmptyEntries);
+            return GetHeaderLine(lines);
+        }
+
+        /// <summary>
+        /// Builds a TSV data row that matches the column layout in the given header.
+        /// Populates Name, Motif/Sequences Inducing Cleavage, and Specificity/Cleavage Specificity columns.
+        /// </summary>
+        private static string BuildDataRow(string header, string name, string motif, string specificity)
+        {
+            var columns = header.Split('\t');
+            var values = new string[columns.Length];
+            for (int i = 0; i < columns.Length; i++)
+            {
+                string col = columns[i].Trim().ToLowerInvariant();
+                if (col == "name")
+                    values[i] = name;
+                else if (col == "motif" || col == "sequences inducing cleavage")
+                    values[i] = motif;
+                else if (col == "specificity" || col == "cleavage specificity")
+                    values[i] = specificity;
+                else
+                    values[i] = "";
+            }
+            return string.Join("\t", values);
+        }
+
+        /// <summary>
+        /// Verifies that custom proteases defined in proteases_custom.tsv are merged
+        /// into the main ProteaseDictionary when LoadDigestionAgents runs.
+        /// </summary>
+        [Test]
+        public static void TestCustomProteasesAreMerged()
+        {
+            // Arrange: write a custom protease to the custom file
+            string customPath = GlobalVariables.CustomProteasePath;
+
+            // Read the header from the standard proteases.tsv
+            var assembly = typeof(ProteaseDictionary).Assembly;
+            string EmbeddedProteaseResourceName = "Proteomics.ProteolyticDigestion.proteases.tsv";
+
+            var stream = assembly.GetManifestResourceStream(EmbeddedProteaseResourceName);
+            string header = GetHeaderLine(stream);
+
+            BackupPath(customPath, out string backupPath, out bool hadExistingCustomFile, out bool hadExistingCustomDirectory);
+
+            try
+            {
+                // Write a custom protease entry
+                var lines = new List<string>
+                {
+                    header,
+                    BuildDataRow(header, "test-custom-protease", "K|", "full")
+                };
+                File.WriteAllLines(customPath, lines);
+
+                // Act: reload
+                GlobalVariables.SetUpGlobalVariables();
+
+                // Assert: the custom protease should be present
+                Assert.That(ProteaseDictionary.Dictionary.ContainsKey("test-custom-protease"), Is.True,
+                    "Custom protease should be merged into the dictionary");
+            }
+            finally
+            {
+                // Restore original custom file
+                RestorePath(customPath, backupPath, hadExistingCustomFile, hadExistingCustomDirectory);
+
+                // Reset state
+                GlobalVariables.SetUpGlobalVariables();
+            }
+        }
+
+        /// <summary>
+        /// Verifies that when a custom protease has the same name as a default protease,
+        /// the default entry wins (is not overwritten by the custom one).
+        /// </summary>
+        [Test]
+        public static void TestDefaultProteaseWinsOnNameCollision()
+        {
+            // Arrange
+            string customPath = GlobalVariables.CustomProteasePath;
+
+            // Read the header from the standard proteases.tsv
+            var assembly = typeof(ProteaseDictionary).Assembly;
+            string EmbeddedProteaseResourceName = "Proteomics.ProteolyticDigestion.proteases.tsv";
+
+            var stream = assembly.GetManifestResourceStream(EmbeddedProteaseResourceName);
+            string header = GetHeaderLine(stream);
+
+            BackupPath(customPath, out string backupPath, out bool hadExistingCustomFile, out bool hadExistingCustomDirectory);
+
+            try
+            {
+                // Write a custom entry with the same name as a default protease ("trypsin")
+                // but with a different cleavage motif (Asp-N style "|D")
+                var lines = new List<string>
+                {
+                    header,
+                    BuildDataRow(header, "trypsin", "|D", "full")
+                };
+                File.WriteAllLines(customPath, lines);
+
+                // Act
+                GlobalVariables.SetUpGlobalVariables();
+
+                // Assert: trypsin should still exist and use the default motif (K|,R|), not |D
+                Assert.That(ProteaseDictionary.Dictionary.ContainsKey("trypsin"), Is.True);
+                var trypsin = ProteaseDictionary.Dictionary["trypsin"];
+
+                // The default trypsin cleaves at K and R; verify it wasn't replaced by the custom |D
+                Assert.That(trypsin.DigestionMotifs.Count, Is.GreaterThanOrEqualTo(2),
+                    "Default trypsin should have at least 2 motifs (K| and R|). If only 1, the custom entry overwrote the default.");
+            }
+            finally
+            {
+                RestorePath(customPath, backupPath, hadExistingCustomFile, hadExistingCustomDirectory);
+
+                GlobalVariables.SetUpGlobalVariables();
+            }
+        }
+
+        /// <summary>
+        /// Verifies that custom RNases defined in rnases_custom.tsv are merged
+        /// into the main RnaseDictionary when LoadDigestionAgents runs.
+        /// </summary>
+        [Test]
+        public static void TestCustomRnasesAreMerged()
+        {
+            // Arrange
+            string customPath = GlobalVariables.CustomRnasePath;
+
+            // Read the header from the standard proteases.tsv
+            var assembly = typeof(RnaseDictionary).Assembly;
+            string EmbeddedProteaseResourceName = "Transcriptomics.Digestion.rnases.tsv";
+
+            var stream = assembly.GetManifestResourceStream(EmbeddedProteaseResourceName);
+            string header = GetHeaderLine(stream);
+
+            BackupPath(customPath, out string backupPath, out bool hadExistingCustomFile, out bool hadExistingCustomDirectory);
+
+            try
+            {
+                var lines = new List<string>
+                {
+                    header,
+                    BuildDataRow(header, "test-custom-rnase", "A|", "full")
+                };
+                File.WriteAllLines(customPath, lines);
+
+                // Act
+                GlobalVariables.SetUpGlobalVariables();
+
+                // Assert
+                Assert.That(RnaseDictionary.Dictionary.ContainsKey("test-custom-rnase"), Is.True,
+                    "Custom RNase should be merged into the dictionary");
+            }
+            finally
+            {
+                RestorePath(customPath, backupPath, hadExistingCustomFile, hadExistingCustomDirectory);
+
+                GlobalVariables.SetUpGlobalVariables();
+            }
+        }
+
+        /// <summary>
+        /// Verifies that when a custom RNase has the same name as a default RNase,
+        /// the default entry wins (is not overwritten by the custom one).
+        /// </summary>
+        [Test]
+        public static void TestDefaultRnaseWinsOnNameCollision()
+        {
+            // Arrange
+            string customPath = GlobalVariables.CustomRnasePath;
+
+            // Read the header from the standard proteases.tsv
+            var assembly = typeof(RnaseDictionary).Assembly;
+            string EmbeddedProteaseResourceName = "Transcriptomics.Digestion.rnases.tsv";
+
+            var stream = assembly.GetManifestResourceStream(EmbeddedProteaseResourceName);
+            string header = GetHeaderLine(stream);
+
+            BackupPath(customPath, out string backupPath, out bool hadExistingCustomFile, out bool hadExistingCustomDirectory);
+
+            try
+            {
+                // Write a custom entry colliding with "RNase T1" (which normally cleaves at G|)
+                // but with a different motif (C|)
+                var lines = new List<string>
+                {
+                    header,
+                    BuildDataRow(header, "RNase T1", "C|", "full")
+                };
+                File.WriteAllLines(customPath, lines);
+
+                // Act
+                GlobalVariables.SetUpGlobalVariables();
+
+                // Assert: RNase T1 should still exist and use the default motif (G|), not C|
+                Assert.That(RnaseDictionary.Dictionary.ContainsKey("RNase T1"), Is.True);
+                var rnaseT1 = RnaseDictionary.Dictionary["RNase T1"];
+
+                // Default RNase T1 cleaves at G; if the custom C| replaced it, there would be
+                // a single motif matching C instead of G
+                Assert.That(rnaseT1.DigestionMotifs.Any(m => m.InducingCleavage == "G"), Is.True,
+                    "Default RNase T1 should retain its G cleavage motif, not be overwritten by the custom entry");
+            }
+            finally
+            {
+                RestorePath(customPath, backupPath, hadExistingCustomFile, hadExistingCustomDirectory);
+
+                GlobalVariables.SetUpGlobalVariables();
+            }
+        }
+
+        /// <summary>
+        /// When proteases_custom.tsv does not exist, LoadDigestionAgents creates it
+        /// with a header line. Verify this behavior.
+        /// </summary>
+        [Test]
+        public static void TestCustomProteaseFileCreatedWhenMissing()
+        {
+            string customPath = GlobalVariables.CustomProteasePath;
+
+            BackupPath(customPath, out string backupPath, out bool hadExistingCustomFile, out bool hadExistingCustomDirectory);
+
+            try
+            {
+                // Remove the custom file
+                if (File.Exists(customPath))
+                    File.Delete(customPath);
+
+                // Act
+                GlobalVariables.SetUpGlobalVariables();
+
+                // Assert: the custom file should now exist with at least a header
+                Assert.That(File.Exists(customPath), Is.True,
+                    "proteases_custom.tsv should be created when it doesn't exist");
+                var lines = File.ReadAllLines(customPath);
+                Assert.That(lines.Length, Is.GreaterThanOrEqualTo(1),
+                    "Custom file should contain at least a header line");
+                Assert.That(lines.Any(l => l.TrimStart().StartsWith("Name\t")), Is.True,
+                    "Custom file should contain the TSV header");
+            }
+            finally
+            {
+                RestorePath(customPath, backupPath, hadExistingCustomFile, hadExistingCustomDirectory);
+
+                GlobalVariables.SetUpGlobalVariables();
+            }
+        }
+
+        /// <summary>
+        /// When rnases_custom.tsv does not exist, LoadDigestionAgents creates it
+        /// with a header line. Verify this behavior.
+        /// </summary>
+        [Test]
+        public static void TestCustomRnaseFileCreatedWhenMissing()
+        {
+            string customPath = GlobalVariables.CustomRnasePath;
+
+            BackupPath(customPath, out string backupPath, out bool hadExistingCustomFile, out bool hadExistingCustomDirectory);
+
+            try
+            {
+                if (File.Exists(customPath))
+                    File.Delete(customPath);
+
+                // Act
+                GlobalVariables.SetUpGlobalVariables();
+
+                // Assert
+                Assert.That(File.Exists(customPath), Is.True,
+                    "rnases_custom.tsv should be created when it doesn't exist");
+                var lines = File.ReadAllLines(customPath);
+                Assert.That(lines.Length, Is.GreaterThanOrEqualTo(1),
+                    "Custom file should contain at least a header line");
+                Assert.That(lines.Any(l => l.TrimStart().StartsWith("Name\t")), Is.True,
+                    "Custom file should contain the TSV header");
+            }
+            finally
+            {
+                RestorePath(customPath, backupPath, hadExistingCustomFile, hadExistingCustomDirectory);
+
+                GlobalVariables.SetUpGlobalVariables();
+            }
+        }
+
+        [Test]
+        public static void TestCustomProteaseLoadCatchIsHitWhenCustomFileIsLocked()
+        {
+            string customPath = GlobalVariables.CustomProteasePath;
+            BackupPath(customPath, out string backupPath, out bool hadExistingFile, out bool hadExistingDirectory);
+
+            try
+            {
+                using var lockedFile = new FileStream(customPath, FileMode.Create, FileAccess.ReadWrite, FileShare.None);
+
+                var ex = Assert.Throws<MetaMorpheusException>(() => InvokeLoadDigestionAgents());
+
+                Assert.That(ex!.Message, Does.Contain("Error loading custom proteases with error message:"));
+                Assert.That(ex.InnerException, Is.Not.Null);
+            }
+            finally
+            {
+                RestorePath(customPath, backupPath, hadExistingFile, hadExistingDirectory);
+                GlobalVariables.SetUpGlobalVariables();
+            }
+        }
+
+        [Test]
+        public static void TestCustomProteaseCreationCatchIsHitWhenCustomPathIsDirectory()
+        {
+            string customPath = GlobalVariables.CustomProteasePath;
+            BackupPath(customPath, out string backupPath, out bool hadExistingFile, out bool hadExistingDirectory);
+
+            try
+            {
+                DeletePathIfExists(customPath);
+                Directory.CreateDirectory(customPath);
+
+                var ex = Assert.Throws<MetaMorpheusException>(() => InvokeLoadDigestionAgents());
+
+                Assert.That(ex!.Message, Does.Contain("Error creating default custom protease file with error message:"));
+                Assert.That(ex.InnerException, Is.Not.Null);
+            }
+            finally
+            {
+                RestorePath(customPath, backupPath, hadExistingFile, hadExistingDirectory);
+                GlobalVariables.SetUpGlobalVariables();
+            }
+        }
+
+        [Test]
+        public static void TestCustomRnaseLoadCatchIsHitWhenCustomFileIsLocked()
+        {
+            string customPath = GlobalVariables.CustomRnasePath;
+            BackupPath(customPath, out string backupPath, out bool hadExistingFile, out bool hadExistingDirectory);
+
+            try
+            {
+                using var lockedFile = new FileStream(customPath, FileMode.Create, FileAccess.ReadWrite, FileShare.None);
+
+                var ex = Assert.Throws<MetaMorpheusException>(() => InvokeLoadDigestionAgents());
+
+                Assert.That(ex!.Message, Does.Contain("Error loading custom rnases with error message:"));
+                Assert.That(ex.InnerException, Is.Not.Null);
+            }
+            finally
+            {
+                RestorePath(customPath, backupPath, hadExistingFile, hadExistingDirectory);
+                GlobalVariables.SetUpGlobalVariables();
+            }
+        }
+
+        [Test]
+        public static void TestCustomRnaseCreationCatchIsHitWhenCustomPathIsDirectory()
+        {
+            string customPath = GlobalVariables.CustomRnasePath;
+            BackupPath(customPath, out string backupPath, out bool hadExistingFile, out bool hadExistingDirectory);
+
+            try
+            {
+                DeletePathIfExists(customPath);
+                Directory.CreateDirectory(customPath);
+
+                var ex = Assert.Throws<MetaMorpheusException>(() => InvokeLoadDigestionAgents());
+
+                Assert.That(ex!.Message, Does.Contain("Error creating default custom rnase file with error message:"));
+                Assert.That(ex.InnerException, Is.Not.Null);
+            }
+            finally
+            {
+                RestorePath(customPath, backupPath, hadExistingFile, hadExistingDirectory);
+                GlobalVariables.SetUpGlobalVariables();
+            }
+        }
+
+      
+    }
+}
diff --git a/MetaMorpheus/Test/MatchIonsOfAllCharges.cs b/MetaMorpheus/Test/MatchIonsOfAllCharges.cs
index 019213cf6..793f76b00 100644
--- a/MetaMorpheus/Test/MatchIonsOfAllCharges.cs
+++ b/MetaMorpheus/Test/MatchIonsOfAllCharges.cs
@@ -106,7 +106,7 @@ public static void TestMatchIonsOfAllChargesBottomUp()
 
             List<DigestionMotif> motifs = new List<DigestionMotif> { new DigestionMotif("K", null, 1, null) };
             Protease protease = new Protease("Custom Protease3", CleavageSpecificity.Full, null, null, motifs);
-            ProteaseDictionary.Dictionary.Add(protease.Name, protease);
+            ProteaseDictionary.Dictionary[protease.Name] = protease;
 
             CommonParameters CommonParameters1 = new CommonParameters(
                 digestionParams: new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1),
diff --git a/MetaMorpheus/Test/MultiProteaseParsimonyTest.cs b/MetaMorpheus/Test/MultiProteaseParsimonyTest.cs
index f2ed124f8..4a1473eb1 100644
--- a/MetaMorpheus/Test/MultiProteaseParsimonyTest.cs
+++ b/MetaMorpheus/Test/MultiProteaseParsimonyTest.cs
@@ -889,7 +889,7 @@ public static void MultiProteaseParsimony_TestingActuallyIndistinguisableProtein
             }
 
             CommonParameters commonParameters_tryp = new CommonParameters(digestionParams: new DigestionParams(protease: "trypsin", minPeptideLength: 1));
-            CommonParameters commonParameters_LysC = new CommonParameters(digestionParams: new DigestionParams(protease: "Lys-C (don't cleave before proline)", minPeptideLength: 1));
+            CommonParameters commonParameters_LysC = new CommonParameters(digestionParams: new DigestionParams(protease: "Lys-C|P", minPeptideLength: 1));
 
             PeptideWithSetModifications pepABCK_1T = new PeptideWithSetModifications(protein: p.ElementAt(0), digestionParams: commonParameters_tryp.DigestionParams, oneBasedStartResidueInProtein: 2, oneBasedEndResidueInProtein: 4, cleavageSpecificity: CleavageSpecificity.Full, peptideDescription: "ABCK", missedCleavages: 0, allModsOneIsNterminus: new Dictionary<int, Modification>(), numFixedMods: 0);
             PeptideWithSetModifications pepABCK_2T = new PeptideWithSetModifications(protein: p.ElementAt(1), digestionParams: commonParameters_tryp.DigestionParams, oneBasedStartResidueInProtein: 6, oneBasedEndResidueInProtein: 8, cleavageSpecificity: CleavageSpecificity.Full, peptideDescription: "ABCK", missedCleavages: 0, allModsOneIsNterminus: new Dictionary<int, Modification>(), numFixedMods: 0);
@@ -1085,4 +1085,4 @@ public static void MultiProteaseParsimony_TestingProteaseSpecificFDRCalculations
 
         }
     }
-}
\ No newline at end of file
+}
diff --git a/MetaMorpheus/Test/Test.csproj b/MetaMorpheus/Test/Test.csproj
index cb576b90f..d36871445 100644
--- a/MetaMorpheus/Test/Test.csproj
+++ b/MetaMorpheus/Test/Test.csproj
@@ -24,7 +24,7 @@
     <PackageReference Include="Microsoft.ML" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
-    <PackageReference Include="mzLib" Version="1.0.577" />
+    <PackageReference Include="mzLib" Version="1.0.578" />
     <PackageReference Include="NUnit" Version="4.1.0" />
     <PackageReference Include="NUnit3TestAdapter" Version="4.6.0" />
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.10.0" />
diff --git a/MetaMorpheus/Test/TestOGlyco.cs b/MetaMorpheus/Test/TestOGlyco.cs
index 31d46d840..798ce5e42 100644
--- a/MetaMorpheus/Test/TestOGlyco.cs
+++ b/MetaMorpheus/Test/TestOGlyco.cs
@@ -612,30 +612,6 @@ public static void OGlycoTest_Run2()
             Directory.Delete(Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData"), true);
         }
 
-        [Test]
-        public static void OGlycoTest_Run3()
-        {
-            //Test search EThcD scan with setting DissociationType ETD.The Oxonium ion always matches, but the filter is user controlled.
-            //The scan is modified to contain no 274 and 292 oxonium ions.
-            var task = Toml.ReadFile<GlycoSearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\GlycoSearchTaskconfig_ETD_Run3.toml"), MetaMorpheusTask.tomlConfig);
-
-            Directory.CreateDirectory(Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData"));
-            DbForTask db = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\FiveMucinFasta.fasta"), false);
-            string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\22-12-14_EclipseOglyco_EThcD_150ms_calRxn_17360.mgf");
-            new EverythingRunnerEngine(new List<(string, MetaMorpheusTask)> { ("Task", task) }, new List<string> { spectraFile }, new List<DbForTask> { db }, Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData")).Run();
-            var resultsPath = File.ReadAllLines(Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData\Task\oglyco.psmtsv"));
-            Assert.That(resultsPath.Length > 1);
-            Directory.Delete(Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData"), true);
-
-            Directory.CreateDirectory(Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData"));
-            var task2 = Toml.ReadFile<GlycoSearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\GlycoSearchTaskconfig_ETD_Run3.toml"), MetaMorpheusTask.tomlConfig);
-            task2._glycoSearchParameters.OxoniumIonFilt = true; //turn on the diagnostic filter
-            new EverythingRunnerEngine(new List<(string, MetaMorpheusTask)> { ("Task", task2) }, new List<string> { spectraFile }, new List<DbForTask> { db }, Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData")).Run();
-            var resultsExist = File.Exists(Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData\Task\oglyco.psmtsv"));
-            Assert.That(!resultsExist);
-            Directory.Delete(Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData"), true);
-        }
-
         //make sure that hyphens in protein names don't produce a crash during protein inference from glycopeptides
         [Test]
         public static void OGlycoTest_Run4()

From 303b2883eeeb3e47ddcf3bda5034d005962d769b Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Tue, 12 May 2026 16:17:17 -0500
Subject: [PATCH 12/26] NonParallelizable

---
 .../Test/MetaDraw/FragmentReanalysisRaceConditionTest.cs       | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/MetaMorpheus/Test/MetaDraw/FragmentReanalysisRaceConditionTest.cs b/MetaMorpheus/Test/MetaDraw/FragmentReanalysisRaceConditionTest.cs
index c0912210c..9ab170ba3 100644
--- a/MetaMorpheus/Test/MetaDraw/FragmentReanalysisRaceConditionTest.cs
+++ b/MetaMorpheus/Test/MetaDraw/FragmentReanalysisRaceConditionTest.cs
@@ -24,6 +24,7 @@ namespace Test.MetaDraw
     internal class FragmentReanalysisRaceConditionTest
     {
         [Test]
+        [NonParallelizable]
         public static void MatchIonsWithNewTypes_ProductsChangedDuringExecution_DoesNotThrow()
         {
             // Load test data similar to TestFragmentationReanalysisViewModel_RematchIons
@@ -94,4 +95,4 @@ public static void MatchIonsWithNewTypes_ProductsChangedDuringExecution_DoesNotT
             Assert.That(caughtException, Is.Null, $"InvalidOperationException thrown: {caughtException?.Message}");
         }
     }
-}
\ No newline at end of file
+}

From 0a3076e3e417942c18807e33ac69a87b0b47bc9b Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 13 May 2026 17:11:26 -0500
Subject: [PATCH 13/26] initial commit

---
 .../SpectrumMatch/MirrorSpectrumMatchPlot.cs  | 43 ++++++++++
 .../SpectrumMatch/SpectrumMatchPlot.cs        | 83 ++++++++++++++++++-
 2 files changed, 125 insertions(+), 1 deletion(-)
 create mode 100644 MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MirrorSpectrumMatchPlot.cs

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MirrorSpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MirrorSpectrumMatchPlot.cs
new file mode 100644
index 000000000..e0d213588
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MirrorSpectrumMatchPlot.cs
@@ -0,0 +1,43 @@
+using System.Collections.Generic;
+using MassSpectrometry;
+using Omics.Fragmentation;
+using Omics.SpectrumMatch;
+using OxyPlot.Wpf;
+using Readers;
+
+namespace GuiFunctions
+{
+    /// <summary>
+    /// Creates a mirror plot comparing two different spectrum matches (PSMs) from two different scans.
+    /// The primary PSM's spectrum and matched fragment ions are displayed above the axis (positive Y),
+    /// while the secondary PSM's spectrum and matched fragment ions are mirrored below the axis (negative Y).
+    /// Useful for visually comparing RNA or peptide sequences to highlight differentiating fragment ions.
+    /// </summary>
+    public class MirrorSpectrumMatchPlot : SpectrumMatchPlot
+    {
+        public MirrorSpectrumMatchPlot(
+            PlotView plotView,
+            SpectrumMatchFromTsv psmA,
+            MsDataScan scanA,
+            List<MatchedFragmentIon> ionsA,
+            SpectrumMatchFromTsv psmB,
+            MsDataScan scanB,
+            List<MatchedFragmentIon> ionsB,
+            bool annotateProperties = true)
+            : base(plotView, psmA, scanA, ionsA)
+        {
+            DrawInvertedSpectrum(scanB);
+
+            AnnotateMirrorIons(isBetaPeptide: false, ionsB);
+
+            AdjustMirrorAxes(scanA, scanB);
+
+            if (annotateProperties)
+            {
+                AnnotateProperties();
+            }
+
+            RefreshChart();
+        }
+    }
+}
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
index 75f1e15f7..1af81ddc4 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
@@ -1,4 +1,4 @@
-using System;
+using System;
 using System.Collections.Generic;
 using System.Globalization;
 using System.Linq;
@@ -14,6 +14,7 @@
 using Annotation = OxyPlot.Annotations.Annotation;
 using FontWeights = OxyPlot.FontWeights;
 using HorizontalAlignment = OxyPlot.HorizontalAlignment;
+using LineSeries = OxyPlot.Series.LineSeries;
 using TextAnnotation = OxyPlot.Annotations.TextAnnotation;
 using VerticalAlignment = OxyPlot.VerticalAlignment;
 
@@ -489,6 +490,86 @@ protected void AnnotateLibraryIons(bool isBetaPeptide, List<MatchedFragmentIon>
             Model.Axes[1].LabelFormatter = DrawnSequence.YAxisLabelFormatter;
         }
 
+        /// <summary>
+        /// Draws a second spectrum's raw peaks with inverted (negative) intensities for mirror plot comparison.
+        /// Each peak is drawn as a vertical line from zero to its negated intensity value.
+        /// </summary>
+        protected void DrawInvertedSpectrum(MsDataScan scan)
+        {
+            var yArray = scan.MassSpectrum.YArray;
+            var xArray = scan.MassSpectrum.XArray;
+
+            var invertedSeries = new LineSeries
+            {
+                Color = MetaDrawSettings.UnannotatedPeakColor,
+                StrokeThickness = MetaDrawSettings.StrokeThicknessUnannotated,
+                LineStyle = LineStyle.Solid
+            };
+
+            for (int i = 0; i < xArray.Length; i++)
+            {
+                double mz = xArray[i];
+                double intensity = -yArray[i];
+                invertedSeries.Points.Add(new DataPoint(mz - 0.0001, 0));
+                invertedSeries.Points.Add(new DataPoint(mz, intensity));
+                invertedSeries.Points.Add(new DataPoint(mz + 0.0001, 0));
+            }
+            Model.Series.Add(invertedSeries);
+        }
+
+        /// <summary>
+        /// Mirrors a set of fragment ions below the zero axis (negative Y) for mirror plot comparison.
+        /// Creates new MatchedFragmentIon objects with negated intensities and annotates them
+        /// using the existing annotation pipeline with useLiteralPassedValues.
+        /// </summary>
+        protected void AnnotateMirrorIons(bool isBetaPeptide, List<MatchedFragmentIon> mirrorIons)
+        {
+            var mirroredIons = new List<MatchedFragmentIon>(mirrorIons.Count);
+            foreach (var ion in mirrorIons)
+            {
+                var product = new Product(
+                    ion.NeutralTheoreticalProduct.ProductType,
+                    ion.NeutralTheoreticalProduct.Terminus,
+                    ion.NeutralTheoreticalProduct.NeutralMass,
+                    ion.NeutralTheoreticalProduct.FragmentNumber,
+                    ion.NeutralTheoreticalProduct.ResiduePosition,
+                    ion.NeutralTheoreticalProduct.NeutralLoss);
+
+                mirroredIons.Add(new MatchedFragmentIon(product, ion.Mz,
+                    -ion.Intensity, ion.Charge));
+            }
+
+            AnnotateMatchedIons(isBetaPeptide, mirroredIons, useLiteralPassedValues: true);
+        }
+
+        /// <summary>
+        /// Adjusts plot axes to accommodate a mirror plot with two spectra:
+        /// Y-axis is made symmetric around zero covering both scans' max intensities,
+        /// X-axis covers the union of both scan windows.
+        /// Applies YAxisLabelFormatter for absolute-value display on negative labels.
+        /// </summary>
+        protected void AdjustMirrorAxes(MsDataScan scanA, MsDataScan scanB)
+        {
+            double maxA = scanA.MassSpectrum.YArray.Max();
+            double maxB = scanB.MassSpectrum.YArray.Max();
+            double maxAbs = Math.Max(maxA, maxB) * 1.3;
+
+            var yAxis = Model.Axes[1];
+            yAxis.Minimum = -maxAbs;
+            yAxis.Maximum = maxAbs;
+            yAxis.AbsoluteMinimum = -maxAbs * 2;
+            yAxis.AbsoluteMaximum = maxAbs * 2;
+            yAxis.LabelFormatter = DrawnSequence.YAxisLabelFormatter;
+
+            double xMin = Math.Min(scanA.ScanWindowRange.Minimum, scanB.ScanWindowRange.Minimum);
+            double xMax = Math.Max(scanA.ScanWindowRange.Maximum, scanB.ScanWindowRange.Maximum);
+            var xAxis = Model.Axes[0];
+            xAxis.Minimum = xMin;
+            xAxis.Maximum = xMax;
+            xAxis.AbsoluteMinimum = xMin - 100;
+            xAxis.AbsoluteMaximum = xMax + 100;
+        }
+
         protected void AnnotateProperties(LibrarySpectrum librarySpectrum = null)
         {
             StringBuilder text = new StringBuilder();

From dac375fe3e2b974d2299b4944272e24882192409 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 13 May 2026 18:18:37 -0500
Subject: [PATCH 14/26] pre change

---
 .../SpectrumMatch/SpectrumMatchPlot.cs        |   6 +-
 .../Test/MetaDraw/RnaMirrorPlotGeneration.cs  | 126 ++++++++++++++++++
 2 files changed, 128 insertions(+), 4 deletions(-)
 create mode 100644 MetaMorpheus/Test/MetaDraw/RnaMirrorPlotGeneration.cs

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
index 1af81ddc4..694a25190 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
@@ -555,19 +555,17 @@ protected void AdjustMirrorAxes(MsDataScan scanA, MsDataScan scanB)
             double maxAbs = Math.Max(maxA, maxB) * 1.3;
 
             var yAxis = Model.Axes[1];
-            yAxis.Minimum = -maxAbs;
-            yAxis.Maximum = maxAbs;
             yAxis.AbsoluteMinimum = -maxAbs * 2;
             yAxis.AbsoluteMaximum = maxAbs * 2;
+            yAxis.Zoom(-maxAbs, maxAbs);
             yAxis.LabelFormatter = DrawnSequence.YAxisLabelFormatter;
 
             double xMin = Math.Min(scanA.ScanWindowRange.Minimum, scanB.ScanWindowRange.Minimum);
             double xMax = Math.Max(scanA.ScanWindowRange.Maximum, scanB.ScanWindowRange.Maximum);
             var xAxis = Model.Axes[0];
-            xAxis.Minimum = xMin;
-            xAxis.Maximum = xMax;
             xAxis.AbsoluteMinimum = xMin - 100;
             xAxis.AbsoluteMaximum = xMax + 100;
+            xAxis.Zoom(xMin, xMax);
         }
 
         protected void AnnotateProperties(LibrarySpectrum librarySpectrum = null)
diff --git a/MetaMorpheus/Test/MetaDraw/RnaMirrorPlotGeneration.cs b/MetaMorpheus/Test/MetaDraw/RnaMirrorPlotGeneration.cs
new file mode 100644
index 000000000..4546d1193
--- /dev/null
+++ b/MetaMorpheus/Test/MetaDraw/RnaMirrorPlotGeneration.cs
@@ -0,0 +1,126 @@
+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Threading;
+using GuiFunctions;
+using MassSpectrometry;
+using NUnit.Framework;
+using Omics.Fragmentation;
+using Omics.SpectrumMatch;
+using OxyPlot;
+using OxyPlot.Wpf;
+using Readers;
+
+namespace Test.MetaDraw
+{
+    [TestFixture, Apartment(ApartmentState.STA)]
+    public class RnaMirrorPlotGeneration
+    {
+        private const string OsmTsvPath = @"D:\Projects\SingleOligoPaperGit\results\burkemers\Search for M-Ions and Adducted Oligos\Task1-Burkemers\AllOSMs.osmtsv";
+        private const string MzmlPathA = @"B:\Users\Burke\RNA\25-06-12_standard_runs_1-5_mix\MS_files\renamed_MS_files_02-26-26\22mer#1-Am.raw";
+        private const string MzmlPathB = @"B:\Users\Burke\RNA\25-06-12_standard_runs_1-5_mix\MS_files\renamed_MS_files_02-26-26\22mer#1-m6A.raw";
+        private const string OutputDir = @"D:\Projects\SingleOligoPaperGit\results\burkemers\Search for M-Ions and Adducted Oligos\MirrorPlots";
+
+        private const string TargetM6A = "UUCAAGUAA[Biological:N6-methyladenosine on A]UCCAGGAUAGGCU";
+        private const string Target2OMe = "UUCAAGUAA[Biological:2'-O-Methyladenosine on A]UCCAGGAUAGGCU";
+
+        [SetUp]
+        public void SetUpMetaDrawSettings()
+        {
+            MetaDrawSettings.ExportType = "png";
+            MetaDrawSettings.CanvasPdfExportDpi = 300;
+            MetaDrawSettings.AnnotationBold = true;
+            MetaDrawSettings.StrokeThicknessAnnotated = 2;
+            MetaDrawSettings.UseShortIonAnnotationsWhenPossible = true;
+
+            MetaDrawSettingsViewModel.Instance.DeselectAllSpectrumDescriptorsCommand.Execute(null);
+            MetaDrawSettings.SpectrumDescription["Protein: "] = true;
+            MetaDrawSettings.SpectrumDescription["Score: "] = true;
+            MetaDrawSettings.SpectrumDescription["Retention Time: "] = true;
+        }
+
+        [Test]
+        public void GenerateMirrorPlots()
+        {
+            // Step 1: Load .osmtsv
+            var parsingParams = new SpectrumMatchParsingParameters
+            {
+                FragmentIonsHavePlaceholderForEnvelope = true,
+                ParseMatchedFragmentIons = true
+            };
+            var allPsms = SpectrumMatchTsvReader.ReadOsmTsv(OsmTsvPath, out var warnings, parsingParams);
+            if (warnings.Count > 0)
+                TestContext.WriteLine($"Warnings loading {OsmTsvPath}: {string.Join("; ", warnings)}");
+            TestContext.WriteLine($"Loaded {allPsms.Count} PSMs from {OsmTsvPath}");
+
+            // Step 2: Filter by target sequences, sort by Score descending
+            var m6aPsms = allPsms.Where(p => p.FullSequence == TargetM6A)
+                .OrderByDescending(p => p.Score).ToList();
+            var twoOMePsms = allPsms.Where(p => p.FullSequence == Target2OMe)
+                .OrderByDescending(p => p.Score).ToList();
+
+            TestContext.WriteLine($"Found {m6aPsms.Count} PSMs for m6A sequence");
+            TestContext.WriteLine($"Found {twoOMePsms.Count} PSMs for 2'-OMe sequence");
+
+            Assert.That(m6aPsms, Is.Not.Empty, $"No PSMs found for sequence: {TargetM6A}");
+            Assert.That(twoOMePsms, Is.Not.Empty, $"No PSMs found for sequence: {Target2OMe}");
+
+            // Step 3: Load spectra (one file per sequence)
+            var msDataFileA = MsDataFileReader.GetDataFile(MzmlPathA).LoadAllStaticData();
+            var msDataFileB = MsDataFileReader.GetDataFile(MzmlPathB).LoadAllStaticData();
+            TestContext.WriteLine($"Loaded spectra from A: {MzmlPathA}");
+            TestContext.WriteLine($"Loaded spectra from B: {MzmlPathB}");
+
+            // Step 4: Pair by index (sorted by score descending)
+            int pairCount = Math.Min(m6aPsms.Count, twoOMePsms.Count);
+            if (m6aPsms.Count != twoOMePsms.Count)
+            {
+                TestContext.WriteLine($"Warning: PSM count mismatch — m6A has {m6aPsms.Count}, " +
+                    $"2'-OMe has {twoOMePsms.Count}. Generating {pairCount} pairs " +
+                    $"(unmatched: {Math.Abs(m6aPsms.Count - twoOMePsms.Count)}).");
+            }
+
+            // Step 5: Generate mirror plots
+            Directory.CreateDirectory(OutputDir);
+            int successfulExports = 0;
+
+            for (int i = 0; i < pairCount; i++)
+            {
+                var psmM6A = m6aPsms[i];
+                var psm2OMe = twoOMePsms[i];
+
+                if (psmM6A.MatchedIons == null || psmM6A.MatchedIons.Count == 0)
+                {
+                    TestContext.WriteLine($"Warning: No matched ions for m6A PSM #{i + 1} (Scan {psmM6A.Ms2ScanNumber}), skipping");
+                    continue;
+                }
+                if (psm2OMe.MatchedIons == null || psm2OMe.MatchedIons.Count == 0)
+                {
+                    TestContext.WriteLine($"Warning: No matched ions for 2'-OMe PSM #{i + 1} (Scan {psm2OMe.Ms2ScanNumber}), skipping");
+                    continue;
+                }
+
+                var scanA = msDataFileA.GetOneBasedScan(psmM6A.Ms2ScanNumber);
+                var scanB = msDataFileB.GetOneBasedScan(psm2OMe.Ms2ScanNumber);
+
+                var plotView = new PlotView();
+                var mirrorPlot = new MirrorSpectrumMatchPlot(
+                    plotView,
+                    psmM6A, scanA, psmM6A.MatchedIons,
+                    psm2OMe, scanB, psm2OMe.MatchedIons);
+
+                var outputPath = Path.Combine(OutputDir,
+                    $"Mirror_Pair{i + 1:D3}_Scan{psmM6A.Ms2ScanNumber}_Score{psmM6A.Score:F1}" +
+                    $"_vs_Scan{psm2OMe.Ms2ScanNumber}_Score{psm2OMe.Score:F1}.png");
+
+                mirrorPlot.ExportToPng(outputPath, 700, 370);
+
+                TestContext.WriteLine($"  [{i + 1}/{pairCount}] Exported: {Path.GetFileName(outputPath)}");
+                successfulExports++;
+            }
+
+            TestContext.WriteLine($"Done. Successfully exported {successfulExports} / {pairCount} mirror plots to: {OutputDir}");
+        }
+    }
+}

From 58f56344eca43c5a68af04b0b30c253658dc5124 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 13 May 2026 18:35:01 -0500
Subject: [PATCH 15/26] draft

---
 MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml       |   9 +-
 MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs    |   4 +
 .../GUI/MetaDraw/MirrorPlotTabView.xaml       | 119 +++++++++++
 .../GUI/MetaDraw/MirrorPlotTabView.xaml.cs    |  63 ++++++
 .../Chimeras/MirrorPlotTabViewModel.cs        | 191 ++++++++++++++++++
 .../MetaDraw/MetaDrawDataLoader.cs            |  20 +-
 .../SpectrumMatch/PeptideSpectrumMatchPlot.cs |   9 +-
 .../SpectrumMatch/SpectrumMatchPlot.cs        | 142 ++++++++++++-
 8 files changed, 552 insertions(+), 5 deletions(-)
 create mode 100644 MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
 create mode 100644 MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
 create mode 100644 MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs

diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml
index 5cdff00d9..5fb46f6fc 100644
--- a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml
+++ b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml
@@ -1,4 +1,4 @@
-<Window x:Class="MetaMorpheusGUI.MetaDraw"
+<Window x:Class="MetaMorpheusGUI.MetaDraw"
         x:Name="MetaDrawWindow"
         xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
         xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
@@ -704,6 +704,13 @@
                 <local:ChimeraAnalysisTabView x:Name="ChimeraAnalysisTabView" />
             </TabItem>
 
+            <!-- Mirror Plot tab -->
+            <TabItem Header="{Binding TabHeader}" IsEnabled="{Binding IsTabEnabled}" Background="DarkGray"
+                     d:DataContext="{d:DesignInstance metaDraw:MirrorPlotTabViewModel, IsDesignTimeCreatable=True}"
+                     DataContext="{Binding MirrorPlotTabViewModel, RelativeSource={RelativeSource AncestorType=Window}}">
+                <local:MirrorPlotTabView x:Name="MirrorPlotTabView" />
+            </TabItem>
+
             <!--Deconvolution Exploration tab-->
             <TabItem Header="{Binding TabHeader}" IsEnabled="{Binding IsTabEnabled}" Background="DarkGray"
                      d:DataContext="{d:DesignInstance guiFunctions:DeconExplorationTabViewModel, IsDesignTimeCreatable=True}"
diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
index fc34667fa..8aa467e36 100644
--- a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
+++ b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
@@ -44,6 +44,7 @@ public partial class MetaDraw : Window
         private static List<string> AcceptedSpectralLibraryFormats = new List<string> { ".msp" };
         private FragmentationReanalysisViewModel FragmentationReanalysisViewModel;
         public ChimeraAnalysisTabViewModel ChimeraAnalysisTabViewModel { get; set; }
+        public MirrorPlotTabViewModel MirrorPlotTabViewModel { get; set; }
         public DeconExplorationTabViewModel DeconExplorationViewModel { get; set; }
         public BioPolymerTabViewModel BioPolymerTabViewModel { get; set; }
 
@@ -61,6 +62,7 @@ public MetaDraw(string[]? filesToLoad = null)
 
             BioPolymerTabViewModel = new BioPolymerTabViewModel(MetaDrawLogic);
             ChimeraAnalysisTabViewModel = new ChimeraAnalysisTabViewModel();
+            MirrorPlotTabViewModel = new MirrorPlotTabViewModel();
             DeconExplorationViewModel = new DeconExplorationTabViewModel(MetaDrawLogic);
 
             propertyView = new DataTable();
@@ -510,6 +512,7 @@ private void RefreshPlotsAfterSettingsChange(object sender, MetaDrawSettingsChan
             {
                 MetaDrawLogic.FilterPsms();
                 ChimeraAnalysisTabViewModel.ProcessChimeraData(MetaDrawLogic.FilteredListOfPsms.ToList(), MetaDrawLogic.MsDataFiles);
+                MirrorPlotTabViewModel.ProcessMirrorData(MetaDrawLogic.FilteredListOfPsms.ToList(), MetaDrawLogic.MsDataFiles);
 
                 foreach (var group in BioPolymerTabViewModel.AllGroups)
                 {
@@ -566,6 +569,7 @@ private async void loadFilesButton_Click(object sender, RoutedEventArgs e)
                 loadPsms: true,
                 loadLibraries: true,
                 chimeraTabViewModel: ChimeraAnalysisTabViewModel,
+                mirrorPlotTabViewModel: MirrorPlotTabViewModel,
                 bioPolymerTabViewModel: BioPolymerTabViewModel,
                 deconExplorationTabViewModel: DeconExplorationViewModel,
                 fragmentationReanalysisViewModel: FragmentationReanalysisViewModel);
diff --git a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
new file mode 100644
index 000000000..722cc0ebf
--- /dev/null
+++ b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
@@ -0,0 +1,119 @@
+<UserControl x:Class="MetaMorpheusGUI.MirrorPlotTabView"
+             xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
+             xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+             xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" 
+             xmlns:d="http://schemas.microsoft.com/expression/blend/2008" 
+             xmlns:local="clr-namespace:MetaMorpheusGUI"
+             xmlns:guiFunctions="clr-namespace:GuiFunctions;assembly=GuiFunctions"
+             xmlns:metaDraw="clr-namespace:GuiFunctions.MetaDraw;assembly=GuiFunctions"
+             xmlns:oxy="http://oxyplot.org/wpf"
+             mc:Ignorable="d" 
+             d:DesignHeight="450" d:DesignWidth="800"
+             d:DataContext="{d:DesignInstance metaDraw:MirrorPlotTabViewModel, IsDesignTimeCreatable=True}">
+
+    <Grid>
+        <Grid.ColumnDefinitions>
+            <ColumnDefinition Width="1.5*" />
+            <ColumnDefinition Width="Auto" />
+            <ColumnDefinition Width="5*" />
+            <ColumnDefinition Width="Auto" />
+            <ColumnDefinition Width="1.5*" />
+        </Grid.ColumnDefinitions>
+        <Grid.RowDefinitions>
+            <RowDefinition Height="*" />
+            <RowDefinition Height="Auto" />
+        </Grid.RowDefinitions>
+
+        <!-- Left PSM Grid (Top Spectrum) -->
+        <Grid Grid.Column="0" Grid.Row="0">
+            <Grid.RowDefinitions>
+                <RowDefinition Height="Auto" />
+                <RowDefinition Height="*" />
+            </Grid.RowDefinitions>
+            <Label Grid.Row="0" Content="Top Spectrum (positive)" FontWeight="Bold"
+                   Padding="4,2" />
+            <DataGrid Grid.Row="1" x:Name="LeftDataGrid"
+                      ItemsSource="{Binding AllFilteredPsms}"
+                      SelectedItem="{Binding SelectedLeftPsm}"
+                      AutoGenerateColumns="False" IsReadOnly="True"
+                      SelectionMode="Single" SelectionUnit="FullRow"
+                      SelectedCellsChanged="LeftDataGrid_SelectedCellsChanged"
+                      VerticalAlignment="Stretch" Margin="0"
+                      CanUserDeleteRows="false" CanUserAddRows="false"
+                      ScrollViewer.CanContentScroll="True">
+                <DataGrid.Columns>
+                    <DataGridTextColumn Header="MS2 Scan" Binding="{Binding Ms2ScanNumber}" Width="60"
+                                        ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                    <DataGridTextColumn Header="Full Sequence" Binding="{Binding FullSequence}" Width="140" />
+                    <DataGridTextColumn Header="Score" Binding="{Binding Score}" Width="55"
+                                        ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                    <DataGridTextColumn Header="Q-Value" Binding="{Binding QValue}" Width="55"
+                                        ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                    <DataGridTextColumn Header="File" Binding="{Binding FileNameWithoutExtension}" Width="Auto" />
+                </DataGrid.Columns>
+            </DataGrid>
+        </Grid>
+
+        <!-- Splitter -->
+        <GridSplitter Grid.Column="1" Grid.Row="0"
+                      HorizontalAlignment="Center" VerticalAlignment="Stretch"
+                      Background="Silver" Width="3" />
+
+        <!-- Center: Mirror Plot with Sequence Canvas Overlays -->
+        <Grid Grid.Column="2" Grid.Row="0">
+            <oxy:PlotView x:Name="MirrorPlotView" FontSize="16" FontStretch="Expanded" Margin="0" />
+
+            <Canvas x:Name="TopSequenceCanvas" VerticalAlignment="Top" HorizontalAlignment="Left"
+                    Height="60" Margin="110,6,0,0" Background="Transparent" />
+
+            <Canvas x:Name="BottomSequenceCanvas" VerticalAlignment="Bottom" HorizontalAlignment="Left"
+                    Height="60" Margin="110,0,0,6" Background="Transparent" />
+        </Grid>
+
+        <!-- Splitter -->
+        <GridSplitter Grid.Column="3" Grid.Row="0"
+                      HorizontalAlignment="Center" VerticalAlignment="Stretch"
+                      Background="Silver" Width="3" />
+
+        <!-- Right PSM Grid (Bottom Spectrum) -->
+        <Grid Grid.Column="4" Grid.Row="0">
+            <Grid.RowDefinitions>
+                <RowDefinition Height="Auto" />
+                <RowDefinition Height="*" />
+            </Grid.RowDefinitions>
+            <Label Grid.Row="0" Content="Bottom Spectrum (mirror)" FontWeight="Bold"
+                   Padding="4,2" />
+            <DataGrid Grid.Row="1" x:Name="RightDataGrid"
+                      ItemsSource="{Binding AllFilteredPsms}"
+                      SelectedItem="{Binding SelectedRightPsm}"
+                      AutoGenerateColumns="False" IsReadOnly="True"
+                      SelectionMode="Single" SelectionUnit="FullRow"
+                      SelectedCellsChanged="RightDataGrid_SelectedCellsChanged"
+                      VerticalAlignment="Stretch" Margin="0"
+                      CanUserDeleteRows="false" CanUserAddRows="false"
+                      ScrollViewer.CanContentScroll="True">
+                <DataGrid.Columns>
+                    <DataGridTextColumn Header="MS2 Scan" Binding="{Binding Ms2ScanNumber}" Width="60"
+                                        ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                    <DataGridTextColumn Header="Full Sequence" Binding="{Binding FullSequence}" Width="140" />
+                    <DataGridTextColumn Header="Score" Binding="{Binding Score}" Width="55"
+                                        ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                    <DataGridTextColumn Header="Q-Value" Binding="{Binding QValue}" Width="55"
+                                        ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                    <DataGridTextColumn Header="File" Binding="{Binding FileNameWithoutExtension}" Width="Auto" />
+                </DataGrid.Columns>
+            </DataGrid>
+        </Grid>
+
+        <!-- Export Bar -->
+        <StackPanel Grid.Row="1" Grid.Column="0" Grid.ColumnSpan="5"
+                    Orientation="Horizontal" HorizontalAlignment="Right" Margin="4">
+            <ComboBox ItemsSource="{Binding ExportTypes, Source={x:Static guiFunctions:MetaDrawSettingsViewModel.Instance}}"
+                      SelectedItem="{Binding ExportType, Source={x:Static guiFunctions:MetaDrawSettingsViewModel.Instance}}"
+                      HorizontalContentAlignment="Center" VerticalContentAlignment="Center"
+                      Width="70" Margin="0,0,5,0" />
+            <Button Content="Export" Command="{Binding ExportCommand}"
+                    Width="80" Margin="5,0" />
+        </StackPanel>
+    </Grid>
+</UserControl>
diff --git a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
new file mode 100644
index 000000000..89108aafa
--- /dev/null
+++ b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
@@ -0,0 +1,63 @@
+using GuiFunctions;
+using GuiFunctions.MetaDraw;
+using System.Windows;
+using System.Windows.Controls;
+
+namespace MetaMorpheusGUI
+{
+    public partial class MirrorPlotTabView : UserControl
+    {
+        public MirrorPlotTabView()
+        {
+            InitializeComponent();
+
+            MirrorPlotView.DataContextChanged += (s, e) =>
+            {
+                if (DataContext is MirrorPlotTabViewModel vm)
+                {
+                    vm.MirrorPlotView = MirrorPlotView;
+                    vm.TopCanvasExport = TopSequenceCanvas;
+                    vm.BottomCanvasExport = BottomSequenceCanvas;
+                }
+            };
+        }
+
+        private void LeftDataGrid_SelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
+        {
+            if (DataContext is MirrorPlotTabViewModel vm && vm.SelectedLeftPsm != null && vm.SelectedRightPsm != null)
+            {
+                RebuildSequences(vm);
+            }
+        }
+
+        private void RightDataGrid_SelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
+        {
+            if (DataContext is MirrorPlotTabViewModel vm && vm.SelectedLeftPsm != null && vm.SelectedRightPsm != null)
+            {
+                RebuildSequences(vm);
+            }
+        }
+
+        private void RebuildSequences(MirrorPlotTabViewModel vm)
+        {
+            TopSequenceCanvas.Children.Clear();
+            BottomSequenceCanvas.Children.Clear();
+
+            var topSequence = new DrawnSequence(TopSequenceCanvas, vm.SelectedLeftPsm, false);
+            topSequence.AnnotateBaseSequence(
+                vm.SelectedLeftPsm.BaseSeq,
+                vm.SelectedLeftPsm.FullSequence,
+                10,
+                vm.SelectedLeftPsm.MatchedIons,
+                vm.SelectedLeftPsm);
+
+            var bottomSequence = new DrawnSequence(BottomSequenceCanvas, vm.SelectedRightPsm, false);
+            bottomSequence.AnnotateBaseSequence(
+                vm.SelectedRightPsm.BaseSeq,
+                vm.SelectedRightPsm.FullSequence,
+                10,
+                vm.SelectedRightPsm.MatchedIons,
+                vm.SelectedRightPsm);
+        }
+    }
+}
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
new file mode 100644
index 000000000..73c7a1605
--- /dev/null
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
@@ -0,0 +1,191 @@
+using System;
+using System.Collections.Generic;
+using System.Collections.ObjectModel;
+using System.IO;
+using System.Linq;
+using System.Threading;
+using System.Windows;
+using System.Windows.Controls;
+using System.Windows.Data;
+using System.Windows.Input;
+using System.Windows.Media;
+using System.Windows.Media.Imaging;
+using GuiFunctions;
+using MassSpectrometry;
+using Omics.Fragmentation;
+using Omics.SpectrumMatch;
+using Readers;
+
+namespace GuiFunctions.MetaDraw;
+
+public class MirrorPlotTabViewModel : MetaDrawTabViewModel
+{
+    public override string TabHeader { get; init; } = "Mirror Plot";
+
+    public ObservableCollection<SpectrumMatchFromTsv> AllFilteredPsms { get; set; }
+
+    private SpectrumMatchFromTsv _selectedLeftPsm;
+    public SpectrumMatchFromTsv SelectedLeftPsm
+    {
+        get => _selectedLeftPsm;
+        set
+        {
+            _selectedLeftPsm = value;
+            OnPropertyChanged(nameof(SelectedLeftPsm));
+            RebuildMirrorPlot();
+        }
+    }
+
+    private SpectrumMatchFromTsv _selectedRightPsm;
+    public SpectrumMatchFromTsv SelectedRightPsm
+    {
+        get => _selectedRightPsm;
+        set
+        {
+            _selectedRightPsm = value;
+            OnPropertyChanged(nameof(SelectedRightPsm));
+            RebuildMirrorPlot();
+        }
+    }
+
+    private PeptideSpectrumMatchPlot _mirrorPlot;
+    public PeptideSpectrumMatchPlot MirrorPlot
+    {
+        get => _mirrorPlot;
+        set
+        {
+            _mirrorPlot = value;
+            OnPropertyChanged(nameof(MirrorPlot));
+        }
+    }
+
+    public Dictionary<string, MsDataFile> MsDataFiles { get; private set; }
+
+    public ICommand ExportCommand { get; set; }
+
+    public MirrorPlotTabViewModel(string exportDirectory = null)
+    {
+        AllFilteredPsms = new ObservableCollection<SpectrumMatchFromTsv>();
+        ExportDirectory = exportDirectory ?? Environment.GetFolderPath(Environment.SpecialFolder.MyDocuments);
+        ExportCommand = new DelegateCommand(obj => ExportPlot());
+        BindingOperations.EnableCollectionSynchronization(AllFilteredPsms, ThreadLocker);
+    }
+
+    public void ProcessMirrorData(List<SpectrumMatchFromTsv> allPsms, Dictionary<string, MsDataFile> dataFiles)
+    {
+        MsDataFiles = dataFiles;
+        AllFilteredPsms.Clear();
+
+        foreach (var psm in allPsms)
+        {
+            AllFilteredPsms.Add(psm);
+        }
+    }
+
+    public void RebuildMirrorPlot()
+    {
+        if (SelectedLeftPsm == null || SelectedRightPsm == null)
+            return;
+
+        if (!MsDataFiles.TryGetValue(SelectedLeftPsm.FileNameWithoutExtension, out var dataFileA))
+            return;
+        if (!MsDataFiles.TryGetValue(SelectedRightPsm.FileNameWithoutExtension, out var dataFileB))
+            return;
+
+        var scanA = dataFileA.GetOneBasedScan(SelectedLeftPsm.Ms2ScanNumber);
+        var scanB = dataFileB.GetOneBasedScan(SelectedRightPsm.Ms2ScanNumber);
+
+        if (scanA == null || scanB == null)
+            return;
+
+        var plotViewRef = MirrorPlotView;
+        if (plotViewRef == null)
+            return;
+
+        MirrorPlot = new PeptideSpectrumMatchPlot(
+            plotViewRef,
+            SelectedLeftPsm,
+            scanA,
+            SelectedLeftPsm.MatchedIons,
+            annotateProperties: false,
+            mirrorIons: SelectedRightPsm.MatchedIons);
+
+        MirrorPlot.AnnotatePropertiesBottom(SelectedRightPsm);
+    }
+
+    public void ExportPlot()
+    {
+        if (MirrorPlot == null || TopCanvasExport == null || BottomCanvasExport == null)
+            return;
+
+        string path = Path.Combine(ExportDirectory,
+            $"MirrorPlot_{SelectedLeftPsm?.Ms2ScanNumber}_{SelectedRightPsm?.Ms2ScanNumber}.{MetaDrawSettings.ExportType.ToLower()}");
+
+        double width = 700;
+        double height = 370;
+        double dpiScale = MetaDrawSettings.CanvasPdfExportDpi / 96.0;
+
+        string tempModelPath = Path.Combine(Path.GetDirectoryName(path), Path.GetRandomFileName() + "." + MetaDrawSettings.ExportType);
+        string tempTopSeqPath = Path.Combine(Path.GetDirectoryName(path), Path.GetRandomFileName() + "_topSeq.png");
+        string tempBottomSeqPath = Path.Combine(Path.GetDirectoryName(path), Path.GetRandomFileName() + "_bottomSeq.png");
+
+        List<System.Drawing.Bitmap> bitmaps = new();
+        List<Point> points = new();
+
+        MirrorPlot.ExportToPng(tempModelPath, (int)width, (int)height);
+        bitmaps.Add(new System.Drawing.Bitmap(tempModelPath));
+        points.Add(new Point(0, 0));
+
+        RenderCanvasToFile(TopCanvasExport, tempTopSeqPath, dpiScale);
+        System.Drawing.Bitmap topBitmap = new(tempTopSeqPath);
+        bitmaps.Add(topBitmap);
+        var topOffset = (Vector)TopCanvasExport.GetType()
+            .GetProperty("VisualOffset", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            .GetValue(TopCanvasExport);
+        points.Add(new Point(topOffset.X, topOffset.Y));
+
+        RenderCanvasToFile(BottomCanvasExport, tempBottomSeqPath, dpiScale);
+        System.Drawing.Bitmap bottomBitmap = new(tempBottomSeqPath);
+        bitmaps.Add(bottomBitmap);
+        var bottomOffset = (Vector)BottomCanvasExport.GetType()
+            .GetProperty("VisualOffset", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+            .GetValue(BottomCanvasExport);
+        points.Add(new Point(bottomOffset.X, bottomOffset.Y));
+
+        System.Drawing.Bitmap combined = MetaDrawLogic.CombineBitmap(bitmaps, points);
+
+        topBitmap.Dispose();
+        bottomBitmap.Dispose();
+        File.Delete(tempModelPath);
+        File.Delete(tempTopSeqPath);
+        File.Delete(tempBottomSeqPath);
+
+        SpectrumMatchPlot.ExportPlot(path, combined, width, height);
+    }
+
+    private static void RenderCanvasToFile(Canvas canvas, string path, double dpiScale)
+    {
+        canvas.Height += 30;
+        canvas.Width += 30;
+        Size size = new((int)canvas.Width, (int)canvas.Height);
+        canvas.Measure(size);
+        canvas.Arrange(new Rect(size));
+
+        RenderTargetBitmap rtb = new(
+            (int)(dpiScale * canvas.Width),
+            (int)(dpiScale * canvas.Height),
+            MetaDrawSettings.CanvasPdfExportDpi,
+            MetaDrawSettings.CanvasPdfExportDpi,
+            PixelFormats.Pbgra32);
+        rtb.Render(canvas);
+
+        PngBitmapEncoder encoder = new();
+        encoder.Frames.Add(BitmapFrame.Create(rtb));
+        using FileStream file = File.Create(path);
+        encoder.Save(file);
+    }
+
+    public OxyPlot.Wpf.PlotView MirrorPlotView { get; set; }
+    public Canvas TopCanvasExport { get; set; }
+    public Canvas BottomCanvasExport { get; set; }
+}
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawDataLoader.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawDataLoader.cs
index 30a3f9701..5f852b1dc 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawDataLoader.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawDataLoader.cs
@@ -1,4 +1,4 @@
-#nullable enable
+#nullable enable
 using EngineLayer;
 using Omics.Fragmentation;
 using Readers.SpectralLibrary;
@@ -35,6 +35,7 @@ public async Task<List<string>> LoadAllAsync(
         bool loadPsms,
         bool loadLibraries,
         ChimeraAnalysisTabViewModel? chimeraTabViewModel = null,
+        MirrorPlotTabViewModel? mirrorPlotTabViewModel = null,
         BioPolymerTabViewModel? bioPolymerTabViewModel = null,
         DeconExplorationTabViewModel? deconExplorationTabViewModel = null,
         FragmentationReanalysisViewModel? fragmentationReanalysisViewModel = null)
@@ -49,6 +50,8 @@ public async Task<List<string>> LoadAllAsync(
         PrepareProgressVisualization(loadSpectra, loadPsms, loadLibraries, _logic);
         if (chimeraTabViewModel is not null) 
             chimeraTabViewModel.IsTabEnabled = false;
+        if (mirrorPlotTabViewModel is not null) 
+            mirrorPlotTabViewModel.IsTabEnabled = false;
         if (bioPolymerTabViewModel is not null) 
             bioPolymerTabViewModel.IsTabEnabled = false;
         if (deconExplorationTabViewModel is not null) 
@@ -108,6 +111,10 @@ public async Task<List<string>> LoadAllAsync(
         {
             Task.Run(() => ProcessChimeraTab(chimeraTabViewModel, outputDirectory, token), token);
         }
+        if (mirrorPlotTabViewModel is not null && _logic.FilteredListOfPsms.Any() && _logic.MsDataFiles.Any())
+        {
+            Task.Run(() => ProcessMirrorTab(mirrorPlotTabViewModel, outputDirectory, token), token);
+        }
 
         return allErrors;
     }
@@ -499,6 +506,17 @@ private void ProcessChimeraTab(ChimeraAnalysisTabViewModel tab, string outDir, C
         tab.IsTabEnabled = true;
     }
 
+    private void ProcessMirrorTab(MirrorPlotTabViewModel tab, string outDir, CancellationToken token)
+    {
+        if (token.IsCancellationRequested)
+            return;
+
+        tab.ProcessMirrorData(_logic.FilteredListOfPsms.ToList(), _logic.MsDataFiles);
+
+        tab.ExportDirectory = outDir;
+        tab.IsTabEnabled = true;
+    }
+
     #endregion
 
     #region UI Progress
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/PeptideSpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/PeptideSpectrumMatchPlot.cs
index 083a71f46..ea22c512f 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/PeptideSpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/PeptideSpectrumMatchPlot.cs
@@ -1,4 +1,4 @@
-using EngineLayer;
+using EngineLayer;
 using MassSpectrometry;
 using System.Collections.Generic;
 using System.IO;
@@ -19,7 +19,7 @@ namespace GuiFunctions
     public class PeptideSpectrumMatchPlot : SpectrumMatchPlot
     {
         public PeptideSpectrumMatchPlot(OxyPlot.Wpf.PlotView plotView, SpectrumMatchFromTsv sm, MsDataScan scan,
-            List<MatchedFragmentIon> matchedFragmentIons, bool annotateProperties = true, LibrarySpectrum librarySpectrum = null, bool stationarySequence = false)
+            List<MatchedFragmentIon> matchedFragmentIons, bool annotateProperties = true, LibrarySpectrum librarySpectrum = null, bool stationarySequence = false, List<MatchedFragmentIon> mirrorIons = null)
             : base(plotView, sm, scan, matchedFragmentIons)
         {
             if (annotateProperties)
@@ -41,6 +41,11 @@ public PeptideSpectrumMatchPlot(OxyPlot.Wpf.PlotView plotView, SpectrumMatchFrom
                 AnnotateLibraryIons(isBetaPeptide: false, librarySpectrum.MatchedFragmentIons);
             }
 
+            if (mirrorIons != null)
+            {
+                AnnotateLibraryIons(isBetaPeptide: false, mirrorIons);
+            }
+
             RefreshChart();
         }
 
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
index 694a25190..c7b238e69 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
@@ -463,7 +463,9 @@ protected void AnnotateLibraryIons(bool isBetaPeptide, List<MatchedFragmentIon>
                 sumOfLibraryIntensities += libraryIon.Intensity;
             }
 
-            double multiplier = -1 * sumOfMatchedIonIntensities / sumOfLibraryIntensities;
+            double multiplier = sumOfLibraryIntensities == 0
+                ? -1
+                : -1 * sumOfMatchedIonIntensities / sumOfLibraryIntensities;
 
             List<MatchedFragmentIon> mirroredLibraryIons = new List<MatchedFragmentIon>();
 
@@ -721,6 +723,144 @@ protected void AnnotateProperties(LibrarySpectrum librarySpectrum = null)
 
             Model.Annotations.Add(annotation);
         }
+
+        internal void AnnotatePropertiesBottom(SpectrumMatchFromTsv psm)
+        {
+            StringBuilder text = new StringBuilder();
+            if (MetaDrawSettings.SpectrumDescription["Precursor Charge: "])
+            {
+                text.Append("Precursor Charge: ");
+                text.Append(psm.PrecursorCharge);
+                text.Append("\r\n");
+            }
+
+            if (MetaDrawSettings.SpectrumDescription["Precursor Mass: "])
+            {
+                text.Append("Precursor Mass: ");
+                text.Append(psm.PrecursorMass.ToString("F3"));
+                text.Append("\r\n");
+            }
+
+            if (MetaDrawSettings.SpectrumDescription["Theoretical Mass: "])
+            {
+                text.Append("Theoretical Mass: ");
+                text.Append(
+                    double.TryParse(psm.MonoisotopicMassString, NumberStyles.Any, CultureInfo.InvariantCulture,
+                        out var monoMass)
+                        ? monoMass.ToString("F3")
+                        : psm.MonoisotopicMassString);
+                text.Append("\r\n");
+            }
+
+            if (MetaDrawSettings.SpectrumDescription["Protein Accession: "])
+            {
+                text.Append("Accession: ");
+                if (psm.Accession.Length > 10)
+                {
+                    text.Append("\r\n   " + psm.Accession);
+                }
+                else
+                    text.Append(psm.Accession);
+
+                text.Append("\r\n");
+            }
+
+            if (psm.Name != null && MetaDrawSettings.SpectrumDescription["Protein: "])
+            {
+                if (GuiGlobalParamsViewModel.Instance.IsRnaMode)
+                    text.Append("Transcript: ");
+                else
+                    text.Append("Protein: ");
+
+                text.Append(psm.Name);
+                text.Append("\r\n");
+            }
+
+            if (MetaDrawSettings.SpectrumDescription["Retention Time: "])
+            {
+                text.Append("Retention Time: ");
+                text.Append(psm.RetentionTime);
+                text.Append("\r\n");
+            }
+
+            if (psm.OneOverK0 != null && MetaDrawSettings.SpectrumDescription["1/K\u2080: "])
+            {
+                text.Append("1/K\u2080: ");
+                text.Append(psm.OneOverK0);
+                text.Append("\r\n");
+            }
+
+            if (MetaDrawSettings.SpectrumDescription["Decoy/Contaminant/Target: "])
+            {
+                text.Append("Decoy/Contaminant/Target: ");
+                text.Append(psm.DecoyContamTarget);
+                text.Append("\r\n");
+            }
+
+            if (MetaDrawSettings.SpectrumDescription["Sequence Length: "])
+            {
+                text.Append("Sequence Length: ");
+                text.Append(psm.BaseSeq.Length.ToString("F3").Split('.')[0]);
+                text.Append("\r\n");
+            }
+
+            if (MetaDrawSettings.SpectrumDescription["Ambiguity Level: "])
+            {
+                text.Append("Ambiguity Level: ");
+                text.Append(psm.AmbiguityLevel);
+                text.Append("\r\n");
+            }
+
+            if (MetaDrawSettings.SpectrumDescription["Score: "])
+            {
+                text.Append("Score: ");
+                text.Append(psm.Score.ToString("F3"));
+                text.Append("\r\n");
+            }
+
+            if (MetaDrawSettings.SpectrumDescription["Q-Value: "])
+            {
+                text.Append("Q-Value: ");
+                text.Append(psm.QValue.ToString("E2"));
+                text.Append("\r\n");
+            }
+
+            if (MetaDrawSettings.SpectrumDescription["PEP: "])
+            {
+                text.Append("PEP: ");
+                text.Append(psm.PEP.ToString("F3"));
+                text.Append("\r\n");
+            }
+
+            if (MetaDrawSettings.SpectrumDescription["PEP Q-Value: "])
+            {
+                text.Append("PEP Q-Value: ");
+                text.Append(psm.PEP_QValue.ToString("F3"));
+                text.Append("\r\n");
+            }
+
+            double fontSize = MetaDrawSettings.SpectrumDescriptionFontSize;
+            string annotationText = text.ToString();
+            double averageCharWidth = 0.48;
+            int maxLineLength = Math.Min(annotationText.Split('\n').Max(line => line.Length), MaxCharactersPerDescriptionLine);
+            double estimatedWidth = fontSize * averageCharWidth * maxLineLength;
+            double xOffset = -estimatedWidth - 10 - (fontSize / 3);
+
+            var annotation = new PlotTextAnnotation()
+            {
+                Text = text.ToString(),
+                XPosition = PlotTextAnnotation.RelativeToX.Right,
+                YPosition = PlotTextAnnotation.RelativeToY.Bottom,
+                FontWeight = 450,
+                X = xOffset,
+                Y = 10,
+                Font = "Arial",
+                FontSize = MetaDrawSettings.SpectrumDescriptionFontSize,
+                TextColor = OxyColors.Black,
+            };
+
+            Model.Annotations.Add(annotation);
+        }
     }
 
     //TODO: move this to mzLib (https://github.com/smith-chem-wisc/mzLib/blob/master/mzPlot/Annotations/PlotTextAnnotation.cs)

From b025eb4f1735b8df4c90bed58948e3c3445f36e2 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 13 May 2026 19:10:21 -0500
Subject: [PATCH 16/26] revise 1

---
 .../GUI/MetaDraw/MirrorPlotTabView.xaml         | 14 ++++++++++----
 .../GUI/MetaDraw/MirrorPlotTabView.xaml.cs      | 14 ++++++--------
 .../MetaDraw/Chimeras/MirrorPlotTabViewModel.cs | 17 ++++++-----------
 .../MetaDraw/SpectrumMatch/MassSpectrumPlot.cs  |  4 ++--
 .../SpectrumMatch/MirrorSpectrumMatchPlot.cs    |  3 ++-
 .../MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs | 17 ++++++++++++++---
 6 files changed, 40 insertions(+), 29 deletions(-)

diff --git a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
index 722cc0ebf..fd6ab7619 100644
--- a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
+++ b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
@@ -61,13 +61,19 @@
 
         <!-- Center: Mirror Plot with Sequence Canvas Overlays -->
         <Grid Grid.Column="2" Grid.Row="0">
-            <oxy:PlotView x:Name="MirrorPlotView" FontSize="16" FontStretch="Expanded" Margin="0" />
+            <Grid.RowDefinitions>
+                <RowDefinition Height="Auto" />
+                <RowDefinition Height="*" />
+                <RowDefinition Height="Auto" />
+            </Grid.RowDefinitions>
 
-            <Canvas x:Name="TopSequenceCanvas" VerticalAlignment="Top" HorizontalAlignment="Left"
+            <Canvas Grid.Row="0" x:Name="TopSequenceCanvas"
                     Height="60" Margin="110,6,0,0" Background="Transparent" />
 
-            <Canvas x:Name="BottomSequenceCanvas" VerticalAlignment="Bottom" HorizontalAlignment="Left"
-                    Height="60" Margin="110,0,0,6" Background="Transparent" />
+            <oxy:PlotView Grid.Row="1" x:Name="MirrorPlotView" FontSize="16" FontStretch="Expanded" Margin="0" />
+
+            <Canvas Grid.Row="2" x:Name="BottomSequenceCanvas"
+                    Height="60" Margin="110,6,0,0" Background="Transparent" />
         </Grid>
 
         <!-- Splitter -->
diff --git a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
index 89108aafa..f9c51e1e4 100644
--- a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
+++ b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
@@ -1,11 +1,9 @@
 using GuiFunctions;
 using GuiFunctions.MetaDraw;
-using System.Windows;
-using System.Windows.Controls;
 
 namespace MetaMorpheusGUI
 {
-    public partial class MirrorPlotTabView : UserControl
+    public partial class MirrorPlotTabView : System.Windows.Controls.UserControl
     {
         public MirrorPlotTabView()
         {
@@ -22,23 +20,23 @@ public MirrorPlotTabView()
             };
         }
 
-        private void LeftDataGrid_SelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
+        private void LeftDataGrid_SelectedCellsChanged(object sender, System.Windows.Controls.SelectedCellsChangedEventArgs e)
         {
             if (DataContext is MirrorPlotTabViewModel vm && vm.SelectedLeftPsm != null && vm.SelectedRightPsm != null)
             {
-                RebuildSequences(vm);
+                DrawSequences(vm);
             }
         }
 
-        private void RightDataGrid_SelectedCellsChanged(object sender, SelectedCellsChangedEventArgs e)
+        private void RightDataGrid_SelectedCellsChanged(object sender, System.Windows.Controls.SelectedCellsChangedEventArgs e)
         {
             if (DataContext is MirrorPlotTabViewModel vm && vm.SelectedLeftPsm != null && vm.SelectedRightPsm != null)
             {
-                RebuildSequences(vm);
+                DrawSequences(vm);
             }
         }
 
-        private void RebuildSequences(MirrorPlotTabViewModel vm)
+        private void DrawSequences(MirrorPlotTabViewModel vm)
         {
             TopSequenceCanvas.Children.Clear();
             BottomSequenceCanvas.Children.Clear();
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
index 73c7a1605..ac9684a63 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
@@ -48,8 +48,8 @@ public SpectrumMatchFromTsv SelectedRightPsm
         }
     }
 
-    private PeptideSpectrumMatchPlot _mirrorPlot;
-    public PeptideSpectrumMatchPlot MirrorPlot
+    private MirrorSpectrumMatchPlot _mirrorPlot;
+    public MirrorSpectrumMatchPlot MirrorPlot
     {
         get => _mirrorPlot;
         set
@@ -75,7 +75,6 @@ public void ProcessMirrorData(List<SpectrumMatchFromTsv> allPsms, Dictionary<str
     {
         MsDataFiles = dataFiles;
         AllFilteredPsms.Clear();
-
         foreach (var psm in allPsms)
         {
             AllFilteredPsms.Add(psm);
@@ -102,15 +101,11 @@ public void RebuildMirrorPlot()
         if (plotViewRef == null)
             return;
 
-        MirrorPlot = new PeptideSpectrumMatchPlot(
+        MirrorPlot = new MirrorSpectrumMatchPlot(
             plotViewRef,
-            SelectedLeftPsm,
-            scanA,
-            SelectedLeftPsm.MatchedIons,
-            annotateProperties: false,
-            mirrorIons: SelectedRightPsm.MatchedIons);
-
-        MirrorPlot.AnnotatePropertiesBottom(SelectedRightPsm);
+            SelectedLeftPsm, scanA, SelectedLeftPsm.MatchedIons,
+            SelectedRightPsm, scanB, SelectedRightPsm.MatchedIons,
+            annotateProperties: true);
     }
 
     public void ExportPlot()
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs
index a46b4d69f..1965b5f8b 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs
@@ -1,4 +1,4 @@
-using System;
+using System;
 using System.Drawing;
 using System.IO;
 using System.Linq;
@@ -21,7 +21,7 @@ public class MassSpectrumPlot : Plot
 {
     private const int MultiLineAnnotationPixelSpacing = 18;
     public PlotView PlotView { get; protected set; }
-    public MsDataScan Scan { get; private set; }
+    public MsDataScan Scan { get; internal set; }
     public MassSpectrumPlot(PlotView plotView, MsDataScan scan) : base(plotView)
     {
         PlotView = plotView;
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MirrorSpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MirrorSpectrumMatchPlot.cs
index e0d213588..6bb840cee 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MirrorSpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MirrorSpectrumMatchPlot.cs
@@ -28,13 +28,14 @@ public MirrorSpectrumMatchPlot(
         {
             DrawInvertedSpectrum(scanB);
 
-            AnnotateMirrorIons(isBetaPeptide: false, ionsB);
+            AnnotateMirrorIons(isBetaPeptide: false, ionsB, psmB, scanB);
 
             AdjustMirrorAxes(scanA, scanB);
 
             if (annotateProperties)
             {
                 AnnotateProperties();
+                AnnotatePropertiesBottom(psmB);
             }
 
             RefreshChart();
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
index c7b238e69..fb0d9d133 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
@@ -524,7 +524,7 @@ protected void DrawInvertedSpectrum(MsDataScan scan)
         /// Creates new MatchedFragmentIon objects with negated intensities and annotates them
         /// using the existing annotation pipeline with useLiteralPassedValues.
         /// </summary>
-        protected void AnnotateMirrorIons(bool isBetaPeptide, List<MatchedFragmentIon> mirrorIons)
+        protected void AnnotateMirrorIons(bool isBetaPeptide, List<MatchedFragmentIon> mirrorIons, SpectrumMatchFromTsv bottomPsm, MsDataScan mirrorScan)
         {
             var mirroredIons = new List<MatchedFragmentIon>(mirrorIons.Count);
             foreach (var ion in mirrorIons)
@@ -537,8 +537,19 @@ protected void AnnotateMirrorIons(bool isBetaPeptide, List<MatchedFragmentIon> m
                     ion.NeutralTheoreticalProduct.ResiduePosition,
                     ion.NeutralTheoreticalProduct.NeutralLoss);
 
-                mirroredIons.Add(new MatchedFragmentIon(product, ion.Mz,
-                    -ion.Intensity, ion.Charge));
+                mirroredIons.Add(new MatchedFragmentIonWithEnvelope(product, ion.Mz,
+                    -ion.Intensity, ion.Charge, null));
+            }
+
+            if (MetaDrawSettings.AnnotateIsotopicEnvelopes && mirrorScan != null)
+            {
+                var savedScan = Scan;
+                var savedPsm = SpectrumMatch;
+                Scan = mirrorScan;
+                SpectrumMatch = bottomPsm;
+                PopulateEnvelopesForScanIfNeeded(mirrorScan, mirroredIons);
+                Scan = savedScan;
+                SpectrumMatch = savedPsm;
             }
 
             AnnotateMatchedIons(isBetaPeptide, mirroredIons, useLiteralPassedValues: true);

From 8744b759e5bb5fd2c5b3539a88817e031ad4b7f7 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 13 May 2026 19:24:47 -0500
Subject: [PATCH 17/26] fix: mirror plot envelope intensities, bottom
 properties Y offset, settings button, and settings re-render

---
 MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs    |  5 +++++
 .../GUI/MetaDraw/MirrorPlotTabView.xaml       |  3 +++
 .../Chimeras/MirrorPlotTabViewModel.cs        |  5 +++++
 .../SpectrumMatch/SpectrumMatchPlot.cs        | 20 +++++++++++++------
 4 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
index 8aa467e36..381901199 100644
--- a/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
+++ b/MetaMorpheus/GUI/MetaDraw/MetaDraw.xaml.cs
@@ -537,6 +537,11 @@ private void RefreshPlotsAfterSettingsChange(object sender, MetaDrawSettingsChan
                 ChimeraAnalysisTabViewModel.ChimeraSpectrumMatchPlot = new ChimeraSpectrumMatchPlot(ChimeraAnalysisTabView.ms2ChimeraPlot, selectedChimeraGroup);
                 ChimeraAnalysisTabViewModel.ChimeraDrawnSequence = new ChimeraDrawnSequence(ChimeraAnalysisTabView.chimeraSequenceCanvas, selectedChimeraGroup, ChimeraAnalysisTabViewModel);
             }
+
+            if (MirrorPlotTabViewModel.SelectedLeftPsm != null && MirrorPlotTabViewModel.SelectedRightPsm != null)
+            {
+                MirrorPlotTabViewModel.RefreshPlot();
+            }
         }
 
         private async void loadFilesButton_Click(object sender, RoutedEventArgs e)
diff --git a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
index fd6ab7619..145c740a0 100644
--- a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
+++ b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
@@ -74,6 +74,9 @@
 
             <Canvas Grid.Row="2" x:Name="BottomSequenceCanvas"
                     Height="60" Margin="110,6,0,0" Background="Transparent" />
+
+            <local:SettingsButtonControl HorizontalAlignment="Left" VerticalAlignment="Top"
+                Panel.ZIndex="1" Margin="4,4,0,0" Width="40" Height="40"/>
         </Grid>
 
         <!-- Splitter -->
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
index ac9684a63..7de2e82f4 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
@@ -108,6 +108,11 @@ public void RebuildMirrorPlot()
             annotateProperties: true);
     }
 
+    public void RefreshPlot()
+    {
+        RebuildMirrorPlot();
+    }
+
     public void ExportPlot()
     {
         if (MirrorPlot == null || TopCanvasExport == null || BottomCanvasExport == null)
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
index fb0d9d133..2e2db768a 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
@@ -256,18 +256,21 @@ private void AnnotateEnvelopePeaks(MatchedFragmentIonWithEnvelope envIon, OxyCol
             var envelope = envIon.Envelope!;
             var product = envIon.NeutralTheoreticalProduct;
 
+            double intensitySign = (useLiteralPassedValues && envIon.Intensity < 0) ? -1 : 1;
+
             // Find the tallest peak in the envelope
-            var tallestPeak = envelope.Peaks.MaxBy(p => p.intensity);
+            var tallestPeak = envelope.Peaks.MaxBy(p => p.intensity * intensitySign);
             if (tallestPeak.intensity == 0)
                 return;
 
             // Annotate all peaks in the envelope
             foreach (var (envMz, envIntensity) in envelope.Peaks)
             {
+                double displayIntensity = envIntensity * intensitySign;
                 bool isTallest = Math.Abs(envMz - tallestPeak.mz) < 0.001 && Math.Abs(envIntensity - tallestPeak.intensity) < 0.001;
 
                 // Draw peak marker (colored)
-                DrawPeak(envMz, envIntensity, MetaDrawSettings.StrokeThicknessAnnotated, ionColor, null);
+                DrawPeak(envMz, displayIntensity, MetaDrawSettings.StrokeThicknessAnnotated, ionColor, null);
 
                 // Draw TEXT annotation only on tallest peak
                 if (isTallest)
@@ -290,8 +293,8 @@ private void AnnotateEnvelopePeaks(MatchedFragmentIonWithEnvelope envIon, OxyCol
                         FontSize = MetaDrawSettings.AnnotatedFontSize,
                         FontWeight = MetaDrawSettings.AnnotationBold ? FontWeights.Bold : 2.0,
                         StrokeThickness = 0,
-                        TextPosition = new DataPoint(envMz, envIntensity),
-                        TextVerticalAlignment = envIntensity < 0 ? VerticalAlignment.Top : VerticalAlignment.Bottom,
+                        TextPosition = new DataPoint(envMz, displayIntensity),
+                        TextVerticalAlignment = displayIntensity < 0 ? VerticalAlignment.Top : VerticalAlignment.Bottom,
                         TextHorizontalAlignment = HorizontalAlignment.Center,
                     };
 
@@ -299,7 +302,7 @@ private void AnnotateEnvelopePeaks(MatchedFragmentIonWithEnvelope envIon, OxyCol
                         ? HiddenAnnotationColor
                         : ionColor;
 
-                    DrawPeak(envMz, envIntensity, MetaDrawSettings.StrokeThicknessAnnotated, ionColor, peakAnnotation);
+                    DrawPeak(envMz, displayIntensity, MetaDrawSettings.StrokeThicknessAnnotated, ionColor, peakAnnotation);
                 }
             }
         }
@@ -857,6 +860,11 @@ internal void AnnotatePropertiesBottom(SpectrumMatchFromTsv psm)
             double estimatedWidth = fontSize * averageCharWidth * maxLineLength;
             double xOffset = -estimatedWidth - 10 - (fontSize / 3);
 
+            double lineSpacing = 1.2;
+            double lineHeight = fontSize * lineSpacing;
+            int lineCount = annotationText.Split('\n').Length;
+            double textHeight = lineCount * lineHeight;
+
             var annotation = new PlotTextAnnotation()
             {
                 Text = text.ToString(),
@@ -864,7 +872,7 @@ internal void AnnotatePropertiesBottom(SpectrumMatchFromTsv psm)
                 YPosition = PlotTextAnnotation.RelativeToY.Bottom,
                 FontWeight = 450,
                 X = xOffset,
-                Y = 10,
+                Y = -(textHeight + 15),
                 Font = "Arial",
                 FontSize = MetaDrawSettings.SpectrumDescriptionFontSize,
                 TextColor = OxyColors.Black,

From a48d8bfebee2196c93d856e529a06c896bc4c34b Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 13 May 2026 19:43:25 -0500
Subject: [PATCH 18/26] feat: relative intensity normalization mode for mirror
 plot

---
 .../GUI/MetaDraw/MirrorPlotTabView.xaml       |  2 +
 .../Chimeras/MirrorPlotTabViewModel.cs        | 80 ++++++++++++++++++-
 2 files changed, 80 insertions(+), 2 deletions(-)

diff --git a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
index 145c740a0..a1dc07aed 100644
--- a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
+++ b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
@@ -117,6 +117,8 @@
         <!-- Export Bar -->
         <StackPanel Grid.Row="1" Grid.Column="0" Grid.ColumnSpan="5"
                     Orientation="Horizontal" HorizontalAlignment="Right" Margin="4">
+            <CheckBox Content="Relative Intensity" IsChecked="{Binding UseRelativeIntensity}"
+                      VerticalContentAlignment="Center" Margin="0,0,10,0" />
             <ComboBox ItemsSource="{Binding ExportTypes, Source={x:Static guiFunctions:MetaDrawSettingsViewModel.Instance}}"
                       SelectedItem="{Binding ExportType, Source={x:Static guiFunctions:MetaDrawSettingsViewModel.Instance}}"
                       HorizontalContentAlignment="Center" VerticalContentAlignment="Center"
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
index 7de2e82f4..4a6fb1f6c 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
@@ -61,6 +61,18 @@ public MirrorSpectrumMatchPlot MirrorPlot
 
     public Dictionary<string, MsDataFile> MsDataFiles { get; private set; }
 
+    private bool _useRelativeIntensity;
+    public bool UseRelativeIntensity
+    {
+        get => _useRelativeIntensity;
+        set
+        {
+            _useRelativeIntensity = value;
+            OnPropertyChanged(nameof(UseRelativeIntensity));
+            RefreshPlot();
+        }
+    }
+
     public ICommand ExportCommand { get; set; }
 
     public MirrorPlotTabViewModel(string exportDirectory = null)
@@ -97,14 +109,30 @@ public void RebuildMirrorPlot()
         if (scanA == null || scanB == null)
             return;
 
+        var ionsA = SelectedLeftPsm.MatchedIons;
+        var ionsB = SelectedRightPsm.MatchedIons;
+
+        if (UseRelativeIntensity)
+        {
+            double maxA = scanA.MassSpectrum.YArray.Max();
+            double maxB = scanB.MassSpectrum.YArray.Max();
+            if (maxA > 0 && maxB > 0)
+            {
+                scanA = NormalizeScan(scanA, maxA);
+                scanB = NormalizeScan(scanB, maxB);
+                ionsA = NormalizeIons(ionsA, maxA);
+                ionsB = NormalizeIons(ionsB, maxB);
+            }
+        }
+
         var plotViewRef = MirrorPlotView;
         if (plotViewRef == null)
             return;
 
         MirrorPlot = new MirrorSpectrumMatchPlot(
             plotViewRef,
-            SelectedLeftPsm, scanA, SelectedLeftPsm.MatchedIons,
-            SelectedRightPsm, scanB, SelectedRightPsm.MatchedIons,
+            SelectedLeftPsm, scanA, ionsA,
+            SelectedRightPsm, scanB, ionsB,
             annotateProperties: true);
     }
 
@@ -188,4 +216,52 @@ private static void RenderCanvasToFile(Canvas canvas, string path, double dpiSca
     public OxyPlot.Wpf.PlotView MirrorPlotView { get; set; }
     public Canvas TopCanvasExport { get; set; }
     public Canvas BottomCanvasExport { get; set; }
+
+    private static MsDataScan NormalizeScan(MsDataScan original, double maxIntensity)
+    {
+        var xArray = original.MassSpectrum.XArray;
+        var normalizedY = new double[xArray.Length];
+        for (int i = 0; i < xArray.Length; i++)
+            normalizedY[i] = original.MassSpectrum.YArray[i] / maxIntensity * 100.0;
+
+        var spectrum = new MzSpectrum(xArray, normalizedY, false);
+        return new MsDataScan(spectrum, original.OneBasedScanNumber, original.MsnOrder,
+            original.IsCentroid, original.Polarity, original.RetentionTime,
+            original.ScanWindowRange, original.ScanFilter, original.MzAnalyzer,
+            original.TotalIonCurrent, original.InjectionTime, original.NoiseData,
+            original.NativeId, original.SelectedIonMZ, original.SelectedIonChargeStateGuess,
+            original.SelectedIonIntensity, original.IsolationMz, original.IsolationWidth,
+            original.DissociationType, original.OneBasedPrecursorScanNumber,
+            original.SelectedIonMonoisotopicGuessMz, original.HcdEnergy,
+            original.ScanDescription, original.CompensationVoltage);
+    }
+
+    private static List<MatchedFragmentIon> NormalizeIons(List<MatchedFragmentIon> ions, double maxIntensity)
+    {
+        var normalized = new List<MatchedFragmentIon>(ions.Count);
+        foreach (var ion in ions)
+        {
+            var product = new Product(
+                ion.NeutralTheoreticalProduct.ProductType,
+                ion.NeutralTheoreticalProduct.Terminus,
+                ion.NeutralTheoreticalProduct.NeutralMass,
+                ion.NeutralTheoreticalProduct.FragmentNumber,
+                ion.NeutralTheoreticalProduct.ResiduePosition,
+                ion.NeutralTheoreticalProduct.NeutralLoss);
+
+            double normalizedIntensity = ion.Intensity / maxIntensity * 100.0;
+
+            if (ion is MatchedFragmentIonWithEnvelope envIon)
+            {
+                normalized.Add(new MatchedFragmentIonWithEnvelope(product, ion.Mz,
+                    normalizedIntensity, ion.Charge, envIon.Envelope));
+            }
+            else
+            {
+                normalized.Add(new MatchedFragmentIon(product, ion.Mz,
+                    normalizedIntensity, ion.Charge));
+            }
+        }
+        return normalized;
+    }
 }

From 0866a7e9180f4da0983be5ed6084785772ed0230 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 13 May 2026 20:24:06 -0500
Subject: [PATCH 19/26] fixes

---
 .../Chimeras/MirrorPlotTabViewModel.cs        | 86 ++++---------------
 .../SpectrumMatch/MassSpectrumPlot.cs         |  4 +-
 2 files changed, 18 insertions(+), 72 deletions(-)

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
index 4a6fb1f6c..37d885b0a 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
@@ -1,15 +1,13 @@
 using System;
 using System.Collections.Generic;
 using System.Collections.ObjectModel;
+using System.Globalization;
 using System.IO;
 using System.Linq;
 using System.Threading;
-using System.Windows;
 using System.Windows.Controls;
 using System.Windows.Data;
 using System.Windows.Input;
-using System.Windows.Media;
-using System.Windows.Media.Imaging;
 using GuiFunctions;
 using MassSpectrometry;
 using Omics.Fragmentation;
@@ -114,8 +112,10 @@ public void RebuildMirrorPlot()
 
         if (UseRelativeIntensity)
         {
-            double maxA = scanA.MassSpectrum.YArray.Max();
-            double maxB = scanB.MassSpectrum.YArray.Max();
+            var yArrayA = scanA.MassSpectrum.YArray;
+            var yArrayB = scanB.MassSpectrum.YArray;
+            double maxA = yArrayA.Max();
+            double maxB = yArrayB.Max();
             if (maxA > 0 && maxB > 0)
             {
                 scanA = NormalizeScan(scanA, maxA);
@@ -143,74 +143,17 @@ public void RefreshPlot()
 
     public void ExportPlot()
     {
-        if (MirrorPlot == null || TopCanvasExport == null || BottomCanvasExport == null)
+        if (MirrorPlot == null)
             return;
 
-        string path = Path.Combine(ExportDirectory,
-            $"MirrorPlot_{SelectedLeftPsm?.Ms2ScanNumber}_{SelectedRightPsm?.Ms2ScanNumber}.{MetaDrawSettings.ExportType.ToLower()}");
+        string directoryPath = Path.Combine(ExportDirectory, "MetaDrawExport",
+            DateTime.Now.ToString("yyyy-MM-dd", CultureInfo.InvariantCulture));
+        Directory.CreateDirectory(directoryPath);
 
-        double width = 700;
-        double height = 370;
-        double dpiScale = MetaDrawSettings.CanvasPdfExportDpi / 96.0;
+        string path = Path.Combine(directoryPath,
+            $"MirrorPlot_Scan{SelectedLeftPsm?.Ms2ScanNumber}_vs_Scan{SelectedRightPsm?.Ms2ScanNumber}.{MetaDrawSettings.ExportType.ToLower()}");
 
-        string tempModelPath = Path.Combine(Path.GetDirectoryName(path), Path.GetRandomFileName() + "." + MetaDrawSettings.ExportType);
-        string tempTopSeqPath = Path.Combine(Path.GetDirectoryName(path), Path.GetRandomFileName() + "_topSeq.png");
-        string tempBottomSeqPath = Path.Combine(Path.GetDirectoryName(path), Path.GetRandomFileName() + "_bottomSeq.png");
-
-        List<System.Drawing.Bitmap> bitmaps = new();
-        List<Point> points = new();
-
-        MirrorPlot.ExportToPng(tempModelPath, (int)width, (int)height);
-        bitmaps.Add(new System.Drawing.Bitmap(tempModelPath));
-        points.Add(new Point(0, 0));
-
-        RenderCanvasToFile(TopCanvasExport, tempTopSeqPath, dpiScale);
-        System.Drawing.Bitmap topBitmap = new(tempTopSeqPath);
-        bitmaps.Add(topBitmap);
-        var topOffset = (Vector)TopCanvasExport.GetType()
-            .GetProperty("VisualOffset", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
-            .GetValue(TopCanvasExport);
-        points.Add(new Point(topOffset.X, topOffset.Y));
-
-        RenderCanvasToFile(BottomCanvasExport, tempBottomSeqPath, dpiScale);
-        System.Drawing.Bitmap bottomBitmap = new(tempBottomSeqPath);
-        bitmaps.Add(bottomBitmap);
-        var bottomOffset = (Vector)BottomCanvasExport.GetType()
-            .GetProperty("VisualOffset", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
-            .GetValue(BottomCanvasExport);
-        points.Add(new Point(bottomOffset.X, bottomOffset.Y));
-
-        System.Drawing.Bitmap combined = MetaDrawLogic.CombineBitmap(bitmaps, points);
-
-        topBitmap.Dispose();
-        bottomBitmap.Dispose();
-        File.Delete(tempModelPath);
-        File.Delete(tempTopSeqPath);
-        File.Delete(tempBottomSeqPath);
-
-        SpectrumMatchPlot.ExportPlot(path, combined, width, height);
-    }
-
-    private static void RenderCanvasToFile(Canvas canvas, string path, double dpiScale)
-    {
-        canvas.Height += 30;
-        canvas.Width += 30;
-        Size size = new((int)canvas.Width, (int)canvas.Height);
-        canvas.Measure(size);
-        canvas.Arrange(new Rect(size));
-
-        RenderTargetBitmap rtb = new(
-            (int)(dpiScale * canvas.Width),
-            (int)(dpiScale * canvas.Height),
-            MetaDrawSettings.CanvasPdfExportDpi,
-            MetaDrawSettings.CanvasPdfExportDpi,
-            PixelFormats.Pbgra32);
-        rtb.Render(canvas);
-
-        PngBitmapEncoder encoder = new();
-        encoder.Frames.Add(BitmapFrame.Create(rtb));
-        using FileStream file = File.Create(path);
-        encoder.Save(file);
+        MirrorPlot.ExportToPng(path, 700, 370);
     }
 
     public OxyPlot.Wpf.PlotView MirrorPlotView { get; set; }
@@ -220,9 +163,10 @@ private static void RenderCanvasToFile(Canvas canvas, string path, double dpiSca
     private static MsDataScan NormalizeScan(MsDataScan original, double maxIntensity)
     {
         var xArray = original.MassSpectrum.XArray;
+        var yArray = original.MassSpectrum.YArray;
         var normalizedY = new double[xArray.Length];
         for (int i = 0; i < xArray.Length; i++)
-            normalizedY[i] = original.MassSpectrum.YArray[i] / maxIntensity * 100.0;
+            normalizedY[i] = yArray[i] / maxIntensity;
 
         var spectrum = new MzSpectrum(xArray, normalizedY, false);
         return new MsDataScan(spectrum, original.OneBasedScanNumber, original.MsnOrder,
@@ -249,7 +193,7 @@ private static List<MatchedFragmentIon> NormalizeIons(List<MatchedFragmentIon> i
                 ion.NeutralTheoreticalProduct.ResiduePosition,
                 ion.NeutralTheoreticalProduct.NeutralLoss);
 
-            double normalizedIntensity = ion.Intensity / maxIntensity * 100.0;
+            double normalizedIntensity = ion.Intensity / maxIntensity;
 
             if (ion is MatchedFragmentIonWithEnvelope envIon)
             {
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs
index 1965b5f8b..651a30eb9 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs
@@ -122,7 +122,8 @@ protected void DrawPeak(double mz, double intensity, double strokeWidth, OxyColo
         if (annotation != null && !annotation.Text.Contains("Miso"))
         {
             var x = annotation.TextPosition.X;
-            var y = annotation.TextPosition.Y + 20;
+            double yOffset = intensity >= 0 ? 20 : -20;
+            var y = annotation.TextPosition.Y + yOffset;
             var splits = annotation.Text.Split('\n');
 
             // Calculate y step for annotation lines based on PlotView's actual height
@@ -130,6 +131,7 @@ protected void DrawPeak(double mz, double intensity, double strokeWidth, OxyColo
             double yRange = yAxis != null ? Math.Abs(yAxis.ActualMaximum - yAxis.ActualMinimum) : 1.0;
             double plotHeight = PlotView?.ActualHeight > 0 ? PlotView.ActualHeight : 370.0; // fallback to default height
             double yStep = yRange * (MultiLineAnnotationPixelSpacing / plotHeight); // Convert pixel spacing to y-axis units
+            if (intensity < 0) yStep = -yStep;
 
             for (int j = splits.Length - 1; j >= 0; j--)
             {

From 94cb1d282796069c593fafffbbab2be95c5932d7 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Wed, 13 May 2026 21:20:49 -0500
Subject: [PATCH 20/26] fixes

---
 .../SpectrumMatch/MassSpectrumPlot.cs         | 22 ++++++++++++++-----
 .../SpectrumMatch/SpectrumMatchPlot.cs        |  4 ++--
 2 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs
index 651a30eb9..fc484fcf6 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/MassSpectrumPlot.cs
@@ -20,6 +20,7 @@ namespace GuiFunctions;
 public class MassSpectrumPlot : Plot
 {
     private const int MultiLineAnnotationPixelSpacing = 18;
+    private const int AnnotationPixelSpacing = 20;
     public PlotView PlotView { get; protected set; }
     public MsDataScan Scan { get; internal set; }
     public MassSpectrumPlot(PlotView plotView, MsDataScan scan) : base(plotView)
@@ -122,15 +123,24 @@ protected void DrawPeak(double mz, double intensity, double strokeWidth, OxyColo
         if (annotation != null && !annotation.Text.Contains("Miso"))
         {
             var x = annotation.TextPosition.X;
-            double yOffset = intensity >= 0 ? 20 : -20;
-            var y = annotation.TextPosition.Y + yOffset;
-            var splits = annotation.Text.Split('\n');
 
-            // Calculate y step for annotation lines based on PlotView's actual height
+            // Calculate y offset in data-coordinates (converted from pixels) so annotations
+            // stay at a consistent visual distance from the peak tip regardless of data scale.
             var yAxis = Model.Axes.FirstOrDefault(a => a.Position == AxisPosition.Left);
             double yRange = yAxis != null ? Math.Abs(yAxis.ActualMaximum - yAxis.ActualMinimum) : 1.0;
-            double plotHeight = PlotView?.ActualHeight > 0 ? PlotView.ActualHeight : 370.0; // fallback to default height
-            double yStep = yRange * (MultiLineAnnotationPixelSpacing / plotHeight); // Convert pixel spacing to y-axis units
+            double plotHeight = PlotView?.ActualHeight > 0 ? PlotView.ActualHeight : 370.0;
+            double yPixelOffset = AnnotationPixelSpacing; // pixels
+
+            double direction = intensity >= 0 ? 1 : -1;
+            double yOffset = yRange * (yPixelOffset * direction / plotHeight);
+            // Cap offset so annotations never float more than 20% of peak height away
+            double yOffsetCap = Math.Abs(intensity) * 0.2;
+            if (Math.Abs(yOffset) > yOffsetCap)
+                yOffset = yOffsetCap * direction;
+            var y = annotation.TextPosition.Y + yOffset;
+            var splits = annotation.Text.Split('\n');
+
+            double yStep = yRange * (MultiLineAnnotationPixelSpacing / plotHeight);
             if (intensity < 0) yStep = -yStep;
 
             for (int j = splits.Length - 1; j >= 0; j--)
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
index 2e2db768a..b3710a4b6 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
@@ -258,8 +258,8 @@ private void AnnotateEnvelopePeaks(MatchedFragmentIonWithEnvelope envIon, OxyCol
 
             double intensitySign = (useLiteralPassedValues && envIon.Intensity < 0) ? -1 : 1;
 
-            // Find the tallest peak in the envelope
-            var tallestPeak = envelope.Peaks.MaxBy(p => p.intensity * intensitySign);
+            // Find the tallest peak in the envelope (by absolute intensity)
+            var tallestPeak = envelope.Peaks.MaxBy(p => p.intensity);
             if (tallestPeak.intensity == 0)
                 return;
 

From bf6c5e79bcd084ced636b7ebc6023e5d628d903c Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Mon, 18 May 2026 17:55:44 -0500
Subject: [PATCH 21/26] test: mark RNA mirror plot generator explicit

---
 MetaMorpheus/Test/MetaDraw/RnaMirrorPlotGeneration.cs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/MetaMorpheus/Test/MetaDraw/RnaMirrorPlotGeneration.cs b/MetaMorpheus/Test/MetaDraw/RnaMirrorPlotGeneration.cs
index 4546d1193..d6d915495 100644
--- a/MetaMorpheus/Test/MetaDraw/RnaMirrorPlotGeneration.cs
+++ b/MetaMorpheus/Test/MetaDraw/RnaMirrorPlotGeneration.cs
@@ -40,7 +40,7 @@ public void SetUpMetaDrawSettings()
             MetaDrawSettings.SpectrumDescription["Retention Time: "] = true;
         }
 
-        [Test]
+        [Test, Explicit("Manual local export utility; depends on machine-specific input files.")]
         public void GenerateMirrorPlots()
         {
             // Step 1: Load .osmtsv

From 5bb90d332a9855d860c533885c84b8bf760e55be Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Mon, 18 May 2026 17:59:11 -0500
Subject: [PATCH 22/26] fix: preserve internal ion metadata in mirror plots

---
 .../Chimeras/MirrorPlotTabViewModel.cs        |  4 ++-
 .../SpectrumMatch/SpectrumMatchPlot.cs        |  4 ++-
 .../Test/MetaDraw/SpectrumMatchPlotTests.cs   | 28 +++++++++++++++++++
 3 files changed, 34 insertions(+), 2 deletions(-)

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
index 37d885b0a..1b0a7c467 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
@@ -191,7 +191,9 @@ private static List<MatchedFragmentIon> NormalizeIons(List<MatchedFragmentIon> i
                 ion.NeutralTheoreticalProduct.NeutralMass,
                 ion.NeutralTheoreticalProduct.FragmentNumber,
                 ion.NeutralTheoreticalProduct.ResiduePosition,
-                ion.NeutralTheoreticalProduct.NeutralLoss);
+                ion.NeutralTheoreticalProduct.NeutralLoss,
+                ion.NeutralTheoreticalProduct.SecondaryProductType,
+                ion.NeutralTheoreticalProduct.SecondaryFragmentNumber);
 
             double normalizedIntensity = ion.Intensity / maxIntensity;
 
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
index b3710a4b6..d42524fa0 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
@@ -538,7 +538,9 @@ protected void AnnotateMirrorIons(bool isBetaPeptide, List<MatchedFragmentIon> m
                     ion.NeutralTheoreticalProduct.NeutralMass,
                     ion.NeutralTheoreticalProduct.FragmentNumber,
                     ion.NeutralTheoreticalProduct.ResiduePosition,
-                    ion.NeutralTheoreticalProduct.NeutralLoss);
+                    ion.NeutralTheoreticalProduct.NeutralLoss,
+                    ion.NeutralTheoreticalProduct.SecondaryProductType,
+                    ion.NeutralTheoreticalProduct.SecondaryFragmentNumber);
 
                 mirroredIons.Add(new MatchedFragmentIonWithEnvelope(product, ion.Mz,
                     -ion.Intensity, ion.Charge, null));
diff --git a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
index 8ffbb8a07..ae411ca53 100644
--- a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
+++ b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
@@ -214,6 +214,34 @@ public void TestPeakColor(PeakAnnotationTestCase testCase)
             Assert.That(annotation.TextColor, Is.EqualTo(testCase.ExpectedColor));
         }
 
+        [Test]
+        public void MirrorPlotRelativeIntensity_PreservesInternalIonClassification()
+        {
+            MetaDrawSettings.DisplayIonAnnotations = true;
+            MetaDrawSettings.DisplayInternalIons = false;
+            MetaDrawSettings.DisplayInternalIonAnnotations = true;
+
+            var mirrorPlotViewModel = new GuiFunctions.MetaDraw.MirrorPlotTabViewModel
+            {
+                MirrorPlotView = new OxyPlot.Wpf.PlotView()
+            };
+
+            mirrorPlotViewModel.ProcessMirrorData(metadrawLogic.FilteredListOfPsms.ToList(), metadrawLogic.MsDataFiles);
+            mirrorPlotViewModel.UseRelativeIntensity = true;
+            mirrorPlotViewModel.SelectedLeftPsm = psm;
+            mirrorPlotViewModel.SelectedRightPsm = psm;
+
+            Assert.That(mirrorPlotViewModel.MirrorPlot, Is.Not.Null);
+
+            var annotationTexts = mirrorPlotViewModel.MirrorPlotView.Model.Annotations
+                .OfType<TextAnnotation>()
+                .Select(p => p.Text)
+                .ToList();
+
+            Assert.That(annotationTexts.Any(p => p.Contains("yIb")), Is.False,
+                "Relative-intensity mirror plot should keep internal ions hidden when internal ion display is disabled.");
+        }
+
         [Test]
         public static void TestCrossLinkSpectrumMatchPlot()
         { 

From 80c2c99f255669e2afeb4b2d1efd37ba0d0684a6 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Mon, 18 May 2026 18:02:39 -0500
Subject: [PATCH 23/26] fix: normalize mirrored isotopic envelopes

---
 .../Chimeras/MirrorPlotTabViewModel.cs        | 11 +++++-
 .../Test/MetaDraw/SpectrumMatchPlotTests.cs   | 36 +++++++++++++++++++
 2 files changed, 46 insertions(+), 1 deletion(-)

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
index 1b0a7c467..f6a395b02 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
@@ -199,8 +199,17 @@ private static List<MatchedFragmentIon> NormalizeIons(List<MatchedFragmentIon> i
 
             if (ion is MatchedFragmentIonWithEnvelope envIon)
             {
+                var normalizedEnvelope = envIon.Envelope is null
+                    ? null
+                    : new IsotopicEnvelope(
+                        envIon.Envelope.Peaks.Select(p => (p.mz, p.intensity / maxIntensity)).ToList(),
+                        envIon.Envelope.MonoisotopicMass,
+                        envIon.Envelope.Charge,
+                        envIon.Envelope.TotalIntensity / maxIntensity,
+                        envIon.Envelope.Peaks.Count);
+
                 normalized.Add(new MatchedFragmentIonWithEnvelope(product, ion.Mz,
-                    normalizedIntensity, ion.Charge, envIon.Envelope));
+                    normalizedIntensity, ion.Charge, normalizedEnvelope));
             }
             else
             {
diff --git a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
index ae411ca53..600710fd8 100644
--- a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
+++ b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
@@ -242,6 +242,42 @@ public void MirrorPlotRelativeIntensity_PreservesInternalIonClassification()
                 "Relative-intensity mirror plot should keep internal ions hidden when internal ion display is disabled.");
         }
 
+        [Test]
+        public void MirrorPlotRelativeIntensity_NormalizesPrePopulatedEnvelopes()
+        {
+            MetaDrawSettings.AnnotateIsotopicEnvelopes = true;
+            MetaDrawSettings.DisplayIonAnnotations = true;
+            MetaDrawSettings.DisplayInternalIons = true;
+
+            var populatedEnvelopePlotView = new OxyPlot.Wpf.PlotView();
+            metadrawLogic.DisplaySpectrumMatch(populatedEnvelopePlotView, psm, parentChildView, out List<string> errors);
+            Assert.That(errors == null || !errors.Any());
+            Assert.That(psm.MatchedIons.OfType<MatchedFragmentIonWithEnvelope>().Any(p => p.Envelope != null), Is.True,
+                "Test setup should populate isotopic envelopes before building the relative-intensity mirror plot.");
+
+            var mirrorPlotViewModel = new GuiFunctions.MetaDraw.MirrorPlotTabViewModel
+            {
+                MirrorPlotView = new OxyPlot.Wpf.PlotView()
+            };
+
+            mirrorPlotViewModel.ProcessMirrorData(metadrawLogic.FilteredListOfPsms.ToList(), metadrawLogic.MsDataFiles);
+            mirrorPlotViewModel.UseRelativeIntensity = true;
+            mirrorPlotViewModel.SelectedLeftPsm = psm;
+            mirrorPlotViewModel.SelectedRightPsm = psm;
+
+            Assert.That(mirrorPlotViewModel.MirrorPlot, Is.Not.Null);
+
+            double maxAbsIntensity = mirrorPlotViewModel.MirrorPlot.Model.Series
+                .OfType<OxyPlot.Series.LineSeries>()
+                .SelectMany(p => p.Points)
+                .Select(p => Math.Abs(p.Y))
+                .DefaultIfEmpty(0)
+                .Max();
+
+            Assert.That(maxAbsIntensity, Is.LessThanOrEqualTo(1.000001),
+                "Relative-intensity mirror plot should normalize already-populated isotopic envelopes.");
+        }
+
         [Test]
         public static void TestCrossLinkSpectrumMatchPlot()
         { 

From fd80e79bc3400bce8d5580bf8de837153f6b3de9 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Mon, 18 May 2026 18:06:22 -0500
Subject: [PATCH 24/26] fix: export the full mirror plot view

---
 .../GUI/MetaDraw/MirrorPlotTabView.xaml       | 22 ++++---
 .../GUI/MetaDraw/MirrorPlotTabView.xaml.cs    |  1 +
 .../Chimeras/MirrorPlotTabViewModel.cs        | 53 +++++++++++++++-
 .../Test/MetaDraw/SpectrumMatchPlotTests.cs   | 63 +++++++++++++++++++
 4 files changed, 127 insertions(+), 12 deletions(-)

diff --git a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
index a1dc07aed..9a345b4b9 100644
--- a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
+++ b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
@@ -61,19 +61,21 @@
 
         <!-- Center: Mirror Plot with Sequence Canvas Overlays -->
         <Grid Grid.Column="2" Grid.Row="0">
-            <Grid.RowDefinitions>
-                <RowDefinition Height="Auto" />
-                <RowDefinition Height="*" />
-                <RowDefinition Height="Auto" />
-            </Grid.RowDefinitions>
+            <Grid x:Name="MirrorPlotExportPanel">
+                <Grid.RowDefinitions>
+                    <RowDefinition Height="Auto" />
+                    <RowDefinition Height="*" />
+                    <RowDefinition Height="Auto" />
+                </Grid.RowDefinitions>
 
-            <Canvas Grid.Row="0" x:Name="TopSequenceCanvas"
-                    Height="60" Margin="110,6,0,0" Background="Transparent" />
+                <Canvas Grid.Row="0" x:Name="TopSequenceCanvas"
+                        Height="60" Margin="110,6,0,0" Background="Transparent" />
 
-            <oxy:PlotView Grid.Row="1" x:Name="MirrorPlotView" FontSize="16" FontStretch="Expanded" Margin="0" />
+                <oxy:PlotView Grid.Row="1" x:Name="MirrorPlotView" FontSize="16" FontStretch="Expanded" Margin="0" />
 
-            <Canvas Grid.Row="2" x:Name="BottomSequenceCanvas"
-                    Height="60" Margin="110,6,0,0" Background="Transparent" />
+                <Canvas Grid.Row="2" x:Name="BottomSequenceCanvas"
+                        Height="60" Margin="110,6,0,0" Background="Transparent" />
+            </Grid>
 
             <local:SettingsButtonControl HorizontalAlignment="Left" VerticalAlignment="Top"
                 Panel.ZIndex="1" Margin="4,4,0,0" Width="40" Height="40"/>
diff --git a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
index f9c51e1e4..3a91418ae 100644
--- a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
+++ b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
@@ -14,6 +14,7 @@ public MirrorPlotTabView()
                 if (DataContext is MirrorPlotTabViewModel vm)
                 {
                     vm.MirrorPlotView = MirrorPlotView;
+                    vm.MirrorPlotExportElement = MirrorPlotExportPanel;
                     vm.TopCanvasExport = TopSequenceCanvas;
                     vm.BottomCanvasExport = BottomSequenceCanvas;
                 }
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
index f6a395b02..2410003cb 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
@@ -8,6 +8,9 @@
 using System.Windows.Controls;
 using System.Windows.Data;
 using System.Windows.Input;
+using System.Windows;
+using System.Windows.Media;
+using System.Windows.Media.Imaging;
 using GuiFunctions;
 using MassSpectrometry;
 using Omics.Fragmentation;
@@ -143,7 +146,7 @@ public void RefreshPlot()
 
     public void ExportPlot()
     {
-        if (MirrorPlot == null)
+        if (MirrorPlot == null || MirrorPlotExportElement == null)
             return;
 
         string directoryPath = Path.Combine(ExportDirectory, "MetaDrawExport",
@@ -153,10 +156,13 @@ public void ExportPlot()
         string path = Path.Combine(directoryPath,
             $"MirrorPlot_Scan{SelectedLeftPsm?.Ms2ScanNumber}_vs_Scan{SelectedRightPsm?.Ms2ScanNumber}.{MetaDrawSettings.ExportType.ToLower()}");
 
-        MirrorPlot.ExportToPng(path, 700, 370);
+        using var bitmap = RenderFrameworkElementToBitmap(MirrorPlotExportElement);
+        SpectrumMatchPlot.ExportPlot(path, bitmap, bitmap.Width, bitmap.Height);
+        MessageBoxHelper.Show(MetaDrawSettings.ExportType + "(s) exported to: " + path);
     }
 
     public OxyPlot.Wpf.PlotView MirrorPlotView { get; set; }
+    public FrameworkElement MirrorPlotExportElement { get; set; }
     public Canvas TopCanvasExport { get; set; }
     public Canvas BottomCanvasExport { get; set; }
 
@@ -219,4 +225,47 @@ private static List<MatchedFragmentIon> NormalizeIons(List<MatchedFragmentIon> i
         }
         return normalized;
     }
+
+    private static System.Drawing.Bitmap RenderFrameworkElementToBitmap(FrameworkElement element)
+    {
+        var dpi = MetaDrawSettings.CanvasPdfExportDpi;
+        var dpiScale = dpi / 96.0;
+
+        int width = (int)Math.Ceiling(element.ActualWidth > 0 ? element.ActualWidth : element.Width);
+        int height = (int)Math.Ceiling(element.ActualHeight > 0 ? element.ActualHeight : element.Height);
+
+        if (width <= 0)
+            width = 700;
+        if (height <= 0)
+            height = 490;
+
+        var size = new Size(width, height);
+        element.Measure(size);
+        element.Arrange(new Rect(size));
+        element.UpdateLayout();
+
+        var renderTargetBitmap = new RenderTargetBitmap(
+            (int)Math.Ceiling(width * dpiScale),
+            (int)Math.Ceiling(height * dpiScale),
+            dpi,
+            dpi,
+            PixelFormats.Pbgra32);
+
+        var drawingVisual = new DrawingVisual();
+        using (var drawingContext = drawingVisual.RenderOpen())
+        {
+            var visualBrush = new VisualBrush(element);
+            drawingContext.DrawRectangle(visualBrush, null, new Rect(new Point(0, 0), size));
+        }
+
+        renderTargetBitmap.Render(drawingVisual);
+
+        var encoder = new PngBitmapEncoder();
+        encoder.Frames.Add(BitmapFrame.Create(renderTargetBitmap));
+
+        using var memoryStream = new System.IO.MemoryStream();
+        encoder.Save(memoryStream);
+        using var temporaryBitmap = new System.Drawing.Bitmap(memoryStream);
+        return new System.Drawing.Bitmap(temporaryBitmap);
+    }
 }
diff --git a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
index 600710fd8..2fd572fc1 100644
--- a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
+++ b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
@@ -4,6 +4,7 @@
 using System.Linq;
 using System.Reflection;
 using System.Threading;
+using System.Windows;
 using System.Windows.Controls;
 using GuiFunctions;
 using NUnit.Framework;
@@ -278,6 +279,68 @@ public void MirrorPlotRelativeIntensity_NormalizesPrePopulatedEnvelopes()
                 "Relative-intensity mirror plot should normalize already-populated isotopic envelopes.");
         }
 
+        [Test]
+        public void MirrorPlotExport_UsesSelectedFormatAndIncludesSequences()
+        {
+            MetaDrawSettings.SuppressMessageBoxes = true;
+            MetaDrawSettings.ExportType = "Jpeg";
+
+            string exportRoot = Path.Combine(outputFolder, "MirrorPlotExportTest");
+            Directory.CreateDirectory(exportRoot);
+
+            var mirrorPlotView = new OxyPlot.Wpf.PlotView
+            {
+                Width = 700,
+                Height = 370
+            };
+            var topCanvas = new Canvas { Width = 700, Height = 60 };
+            var bottomCanvas = new Canvas { Width = 700, Height = 60 };
+            var exportGrid = new Grid
+            {
+                Width = 700,
+                Height = 490
+            };
+            exportGrid.RowDefinitions.Add(new RowDefinition { Height = new GridLength(60) });
+            exportGrid.RowDefinitions.Add(new RowDefinition { Height = new GridLength(370) });
+            exportGrid.RowDefinitions.Add(new RowDefinition { Height = new GridLength(60) });
+            Grid.SetRow(topCanvas, 0);
+            Grid.SetRow(mirrorPlotView, 1);
+            Grid.SetRow(bottomCanvas, 2);
+            exportGrid.Children.Add(topCanvas);
+            exportGrid.Children.Add(mirrorPlotView);
+            exportGrid.Children.Add(bottomCanvas);
+
+            var mirrorPlotViewModel = new GuiFunctions.MetaDraw.MirrorPlotTabViewModel(exportRoot)
+            {
+                MirrorPlotView = mirrorPlotView,
+                MirrorPlotExportElement = exportGrid,
+                TopCanvasExport = topCanvas,
+                BottomCanvasExport = bottomCanvas
+            };
+
+            mirrorPlotViewModel.ProcessMirrorData(metadrawLogic.FilteredListOfPsms.ToList(), metadrawLogic.MsDataFiles);
+            mirrorPlotViewModel.SelectedLeftPsm = psm;
+            mirrorPlotViewModel.SelectedRightPsm = psm;
+
+            Assert.That(mirrorPlotViewModel.MirrorPlot, Is.Not.Null);
+
+            mirrorPlotViewModel.ExportPlot();
+
+            string exportDirectory = Path.Combine(exportRoot, "MetaDrawExport", DateTime.Now.ToString("yyyy-MM-dd"));
+            string exportPath = Path.Combine(exportDirectory,
+                $"MirrorPlot_Scan{psm.Ms2ScanNumber}_vs_Scan{psm.Ms2ScanNumber}.jpeg");
+
+            Assert.That(File.Exists(exportPath), Is.True);
+
+            using var exportStream = File.OpenRead(exportPath);
+            Assert.That(exportStream.ReadByte(), Is.EqualTo(0xFF));
+            Assert.That(exportStream.ReadByte(), Is.EqualTo(0xD8));
+
+            using var exportedImage = System.Drawing.Image.FromFile(exportPath);
+            Assert.That(exportedImage.Height, Is.GreaterThan(370),
+                "Mirror plot export should include the sequence canvases in addition to the plot itself.");
+        }
+
         [Test]
         public static void TestCrossLinkSpectrumMatchPlot()
         { 

From bcbb4cae179547c102198269ca0f343631005029 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Mon, 18 May 2026 18:10:59 -0500
Subject: [PATCH 25/26] fix: refresh mirror sequences with settings

---
 .../GUI/MetaDraw/MirrorPlotTabView.xaml.cs    | 26 ++-------------
 .../Chimeras/MirrorPlotTabViewModel.cs        | 29 +++++++++++++++++
 .../Test/MetaDraw/SpectrumMatchPlotTests.cs   | 32 +++++++++++++++++++
 3 files changed, 63 insertions(+), 24 deletions(-)

diff --git a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
index 3a91418ae..629428f4a 100644
--- a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
+++ b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml.cs
@@ -25,7 +25,7 @@ private void LeftDataGrid_SelectedCellsChanged(object sender, System.Windows.Con
         {
             if (DataContext is MirrorPlotTabViewModel vm && vm.SelectedLeftPsm != null && vm.SelectedRightPsm != null)
             {
-                DrawSequences(vm);
+                vm.RefreshSequences();
             }
         }
 
@@ -33,30 +33,8 @@ private void RightDataGrid_SelectedCellsChanged(object sender, System.Windows.Co
         {
             if (DataContext is MirrorPlotTabViewModel vm && vm.SelectedLeftPsm != null && vm.SelectedRightPsm != null)
             {
-                DrawSequences(vm);
+                vm.RefreshSequences();
             }
         }
-
-        private void DrawSequences(MirrorPlotTabViewModel vm)
-        {
-            TopSequenceCanvas.Children.Clear();
-            BottomSequenceCanvas.Children.Clear();
-
-            var topSequence = new DrawnSequence(TopSequenceCanvas, vm.SelectedLeftPsm, false);
-            topSequence.AnnotateBaseSequence(
-                vm.SelectedLeftPsm.BaseSeq,
-                vm.SelectedLeftPsm.FullSequence,
-                10,
-                vm.SelectedLeftPsm.MatchedIons,
-                vm.SelectedLeftPsm);
-
-            var bottomSequence = new DrawnSequence(BottomSequenceCanvas, vm.SelectedRightPsm, false);
-            bottomSequence.AnnotateBaseSequence(
-                vm.SelectedRightPsm.BaseSeq,
-                vm.SelectedRightPsm.FullSequence,
-                10,
-                vm.SelectedRightPsm.MatchedIons,
-                vm.SelectedRightPsm);
-        }
     }
 }
diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
index 2410003cb..96c9765ee 100644
--- a/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
+++ b/MetaMorpheus/GuiFunctions/MetaDraw/Chimeras/MirrorPlotTabViewModel.cs
@@ -142,6 +142,35 @@ public void RebuildMirrorPlot()
     public void RefreshPlot()
     {
         RebuildMirrorPlot();
+        RefreshSequences();
+    }
+
+    public void RefreshSequences()
+    {
+        TopCanvasExport?.Children.Clear();
+        BottomCanvasExport?.Children.Clear();
+
+        if (TopCanvasExport == null || BottomCanvasExport == null)
+            return;
+
+        if (SelectedLeftPsm == null || SelectedRightPsm == null)
+            return;
+
+        var topSequence = new DrawnSequence(TopCanvasExport, SelectedLeftPsm, false);
+        topSequence.AnnotateBaseSequence(
+            SelectedLeftPsm.BaseSeq,
+            SelectedLeftPsm.FullSequence,
+            10,
+            SelectedLeftPsm.MatchedIons,
+            SelectedLeftPsm);
+
+        var bottomSequence = new DrawnSequence(BottomCanvasExport, SelectedRightPsm, false);
+        bottomSequence.AnnotateBaseSequence(
+            SelectedRightPsm.BaseSeq,
+            SelectedRightPsm.FullSequence,
+            10,
+            SelectedRightPsm.MatchedIons,
+            SelectedRightPsm);
     }
 
     public void ExportPlot()
diff --git a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
index 2fd572fc1..1fea51c9e 100644
--- a/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
+++ b/MetaMorpheus/Test/MetaDraw/SpectrumMatchPlotTests.cs
@@ -341,6 +341,38 @@ public void MirrorPlotExport_UsesSelectedFormatAndIncludesSequences()
                 "Mirror plot export should include the sequence canvases in addition to the plot itself.");
         }
 
+        [Test]
+        public void MirrorPlotRefreshPlot_RedrawsSequencesAfterSettingsChange()
+        {
+            MetaDrawSettings.DrawMatchedIons = true;
+
+            var mirrorPlotViewModel = new GuiFunctions.MetaDraw.MirrorPlotTabViewModel
+            {
+                MirrorPlotView = new OxyPlot.Wpf.PlotView(),
+                TopCanvasExport = new Canvas(),
+                BottomCanvasExport = new Canvas()
+            };
+
+            mirrorPlotViewModel.ProcessMirrorData(metadrawLogic.FilteredListOfPsms.ToList(), metadrawLogic.MsDataFiles);
+            mirrorPlotViewModel.SelectedLeftPsm = psm;
+            mirrorPlotViewModel.SelectedRightPsm = psm;
+            mirrorPlotViewModel.RefreshSequences();
+
+            int initialTopChildCount = mirrorPlotViewModel.TopCanvasExport.Children.Count;
+            int initialBottomChildCount = mirrorPlotViewModel.BottomCanvasExport.Children.Count;
+
+            Assert.That(initialTopChildCount, Is.GreaterThan(0));
+            Assert.That(initialBottomChildCount, Is.GreaterThan(0));
+
+            MetaDrawSettings.DrawMatchedIons = false;
+            mirrorPlotViewModel.RefreshPlot();
+
+            Assert.That(mirrorPlotViewModel.TopCanvasExport.Children.Count, Is.LessThan(initialTopChildCount),
+                "RefreshPlot should redraw the top mirror sequence canvas when sequence-display settings change.");
+            Assert.That(mirrorPlotViewModel.BottomCanvasExport.Children.Count, Is.LessThan(initialBottomChildCount),
+                "RefreshPlot should redraw the bottom mirror sequence canvas when sequence-display settings change.");
+        }
+
         [Test]
         public static void TestCrossLinkSpectrumMatchPlot()
         { 

From 6c626a4c26dd161de85ac1dfd47cad397f2b97d4 Mon Sep 17 00:00:00 2001
From: nbollis <nbollis@comcast.net>
Date: Fri, 3 Jul 2026 10:43:24 -0500
Subject: [PATCH 26/26] more things in table

---
 .../ses_11f53df9effeMffN1QwBnnQeDL.json                | 10 ++++++++++
 MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml       |  8 ++++++++
 2 files changed, 18 insertions(+)
 create mode 100644 .omo/run-continuation/ses_11f53df9effeMffN1QwBnnQeDL.json

diff --git a/.omo/run-continuation/ses_11f53df9effeMffN1QwBnnQeDL.json b/.omo/run-continuation/ses_11f53df9effeMffN1QwBnnQeDL.json
new file mode 100644
index 000000000..328dfb545
--- /dev/null
+++ b/.omo/run-continuation/ses_11f53df9effeMffN1QwBnnQeDL.json
@@ -0,0 +1,10 @@
+{
+  "sessionID": "ses_11f53df9effeMffN1QwBnnQeDL",
+  "updatedAt": "2026-06-19T16:47:34.897Z",
+  "sources": {
+    "background-task": {
+      "state": "idle",
+      "updatedAt": "2026-06-19T16:47:34.897Z"
+    }
+  }
+}
\ No newline at end of file
diff --git a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
index 9a345b4b9..69f0db0c9 100644
--- a/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
+++ b/MetaMorpheus/GUI/MetaDraw/MirrorPlotTabView.xaml
@@ -47,6 +47,10 @@
                     <DataGridTextColumn Header="Full Sequence" Binding="{Binding FullSequence}" Width="140" />
                     <DataGridTextColumn Header="Score" Binding="{Binding Score}" Width="55"
                                         ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                    <DataGridTextColumn Header="Name" Binding="{Binding Name}" Width="55"
+                                        ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                    <DataGridTextColumn Header="Charge" Binding="{Binding ChargeState}" Width="55"
+                                        ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
                     <DataGridTextColumn Header="Q-Value" Binding="{Binding QValue}" Width="55"
                                         ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
                     <DataGridTextColumn Header="File" Binding="{Binding FileNameWithoutExtension}" Width="Auto" />
@@ -109,6 +113,10 @@
                     <DataGridTextColumn Header="Full Sequence" Binding="{Binding FullSequence}" Width="140" />
                     <DataGridTextColumn Header="Score" Binding="{Binding Score}" Width="55"
                                         ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                    <DataGridTextColumn Header="Name" Binding="{Binding Name}" Width="55"
+                                        ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
+                    <DataGridTextColumn Header="Charge" Binding="{Binding ChargeState}" Width="55"
+                                        ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
                     <DataGridTextColumn Header="Q-Value" Binding="{Binding QValue}" Width="55"
                                         ElementStyle="{StaticResource DataGridCenteredCellStyle}" />
                     <DataGridTextColumn Header="File" Binding="{Binding FileNameWithoutExtension}" Width="Auto" />