diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
index 12a517324..a243c156f 100644
--- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
+++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml
@@ -417,6 +417,8 @@
                                     <ToolTip Content="Label-free quantification is performed with FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500" />
                                 </ToolTipService.ToolTip>
                             </RadioButton>
+                            <CheckBox x:Name="CheckBoxUseSharedPeptidesForQuant" Content="Use shared peptides for protein quantification" IsEnabled="True" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500">
+                            </CheckBox>
                             <RadioButton x:Name="CheckBoxSILAC" Content="SILAC/SILAM: Quantify peptides/proteins with stable isotope labels" GroupName="QuantType" Click="CheckBoxSILAC_Checked">
                                 <ToolTipService.ToolTip>
                                     <ToolTip Content="SILAC quantification is performed using FlashLFQ" ToolTipService.ShowDuration="999999" ToolTipService.InitialShowDelay="500"/>
diff --git a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
index e39d52ea4..678e1392c 100644
--- a/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
+++ b/MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs
@@ -189,6 +189,7 @@ private void UpdateFieldsFromTask(SearchTask task)
             CheckBoxNoOneHitWonders.IsChecked = task.SearchParameters.NoOneHitWonders;
             CheckBoxNoQuant.IsChecked = !task.SearchParameters.DoLabelFreeQuantification;
             CheckBoxLFQ.IsChecked = task.SearchParameters.DoLabelFreeQuantification;
+            CheckBoxUseSharedPeptidesForQuant.IsChecked = task.SearchParameters.UseSharedPeptidesForLFQ;
             CheckBoxMultiplex.IsChecked = task.SearchParameters.DoMultiplexQuantification;
             MultiplexComboBox.SelectedItem = task.SearchParameters.MultiplexModId ?? _defaultMultiplexType;
             // If Spectral Recovery is enabled
@@ -626,6 +627,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             TheTask.SearchParameters.DoParsimony = CheckBoxParsimony.IsChecked.Value;
             TheTask.SearchParameters.NoOneHitWonders = CheckBoxNoOneHitWonders.IsChecked.Value;
             TheTask.SearchParameters.DoLabelFreeQuantification = !CheckBoxNoQuant.IsChecked.Value;
+            TheTask.SearchParameters.UseSharedPeptidesForLFQ = CheckBoxUseSharedPeptidesForQuant.IsChecked.Value;
             TheTask.SearchParameters.DoSpectralRecovery = CheckBoxLFQwSpectralRecovery.IsChecked.Value;
             TheTask.SearchParameters.DoMultiplexQuantification = CheckBoxMultiplex.IsChecked.Value;
             TheTask.SearchParameters.MultiplexModId = (string)MultiplexComboBox.SelectedItem;
diff --git a/MetaMorpheus/GUI/Views/CustomFragmentationWindow.xaml.cs b/MetaMorpheus/GUI/Views/CustomFragmentationWindow.xaml.cs
index c123810e2..7c64f353c 100644
--- a/MetaMorpheus/GUI/Views/CustomFragmentationWindow.xaml.cs
+++ b/MetaMorpheus/GUI/Views/CustomFragmentationWindow.xaml.cs
@@ -32,10 +32,10 @@ public CustomFragmentationWindow(List<ProductType> list, bool isRna = false)
             if (list != null)
             {
                 var res = TheList.Where(n => list.Contains(n.Type));
-                foreach(var r in res)
+                foreach (var r in res)
                 {
                     r.IsSelected = true;
-                }               
+                }
             }
 
             base.Closing += this.OnClosing;
@@ -126,17 +126,17 @@ private void OnClosing(object sender, CancelEventArgs e)
         {
             // this window only closes when task is added
             if (this.Visibility == Visibility.Visible)
-            { 
+            {
                 this.Visibility = Visibility.Hidden;
                 e.Cancel = true;
             }
         }
     }
 
-    public class BoolStringClass 
+    public class BoolStringClass
     {
         public ProductType Type { get; set; }
         public bool IsSelected { get; set; }
         public string ToolTip { get; set; }
     }
-}
+}
\ No newline at end of file
diff --git a/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs b/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs
index 057f4fb48..d396b1d28 100644
--- a/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs
+++ b/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs
@@ -588,6 +588,7 @@ private void QuantificationAnalysis()
                 ppmTolerance: Parameters.SearchParameters.QuantifyPpmTol,
                 matchBetweenRunsPpmTolerance: Parameters.SearchParameters.QuantifyPpmTol,  // If these tolerances are not equivalent, then MBR will falsely classify peptides found in the initial search as MBR peaks
                 matchBetweenRuns: Parameters.SearchParameters.MatchBetweenRuns,
+                useSharedPeptidesForProteinQuant: Parameters.SearchParameters.UseSharedPeptidesForLFQ,
                 silent: true,
                 maxThreads: CommonParameters.MaxThreadsToUsePerFile);
 
diff --git a/MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs b/MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs
index c11c69212..080ee2c6d 100644
--- a/MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs
+++ b/MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs
@@ -16,6 +16,7 @@ public SearchParameters()
             NoOneHitWonders = false;
             ModPeptidesAreDifferent = false;
             DoLabelFreeQuantification = true;
+            UseSharedPeptidesForLFQ = false;
             DoSpectralRecovery = false;
             QuantifyPpmTol = 5;
             SearchTarget = true;
@@ -76,6 +77,7 @@ public SearchParameters()
         public bool KeepAllUniprotMods { get; set; }
         public bool DoLocalizationAnalysis { get; set; }
         public bool DoLabelFreeQuantification { get; set; }
+        public bool UseSharedPeptidesForLFQ { get; set; }
         public bool DoMultiplexQuantification { get; set; }
         public string MultiplexModId { get; set; }
         public bool DoSpectralRecovery { get; set; }