diff --git a/MetaMorpheus/EngineLayer/GlobalVariables.cs b/MetaMorpheus/EngineLayer/GlobalVariables.cs
index 96efe5960..bf3c7516a 100644
--- a/MetaMorpheus/EngineLayer/GlobalVariables.cs
+++ b/MetaMorpheus/EngineLayer/GlobalVariables.cs
@@ -1,5 +1,6 @@
 using Chemistry;
 using MassSpectrometry;
+using MzLibUtil;
 using Nett;
 using Proteomics;
 using Proteomics.AminoAcidPolymer;
@@ -14,6 +15,7 @@
 using Omics.Modifications;
 using TopDownProteomics;
 using UsefulProteomicsDatabases;
+using Omics.Digestion;
 
 namespace EngineLayer
 {
@@ -79,6 +81,7 @@ public static void SetUpGlobalVariables()
             SetUpGlobalSettings();
             LoadDissociationTypes();
             LoadAvailableProteomes();
+            LoadCustomProtease();
         }
 
         public static void AddMods(IEnumerable<Modification> modifications, bool modsAreFromTheTopOfProteinXml)
@@ -202,6 +205,32 @@ public static void LoadCustomAminoAcids()
             }
         }
 
+        public static void LoadCustomProtease()
+        {
+            string ProtDirectory = Path.Combine(DataDir, @"ProteolyticDigestion");
+            string customProteasePath = Path.Combine(ProtDirectory, @"CustomProtease.tsv");
+            //load proteases from customProtease file or the original file to Protease dictionary
+            if (File.Exists(customProteasePath))
+            {
+                string[] proteaseToAdd = File.ReadAllLines(customProteasePath);
+                for (int i = 1; i < proteaseToAdd.Length; i++)
+                {
+                    string[] array = proteaseToAdd[i].Split('\t');
+                    List<DigestionMotif> motifList = DigestionMotif.ParseDigestionMotifsFromString(array[1]);
+                    string name = array[0];
+                    CleavageSpecificity cleavageSpecificity = (CleavageSpecificity)Enum.Parse(typeof(CleavageSpecificity), array[4], ignoreCase: true);
+                    string psiMSAccessionNumber = array[5];
+                    string psiMSName = array[6];
+                    string proteaseModDetails = array[8];
+                    Protease protease = new Protease(name, cleavageSpecificity, psiMSAccessionNumber, psiMSName, motifList);
+                    if (!ProteaseDictionary.Dictionary.ContainsKey(protease.Name))
+                    {
+                        ProteaseDictionary.Dictionary.Add(protease.Name, protease);
+                    }
+                }
+            }
+        }
+    
         public static void WriteAminoAcidsFile()
         {
             string directory = Path.Combine(DataDir, @"CustomAminoAcids");
diff --git a/MetaMorpheus/GUI/MainWindow.xaml b/MetaMorpheus/GUI/MainWindow.xaml
index 7c33fd33b..eaa62dcfc 100644
--- a/MetaMorpheus/GUI/MainWindow.xaml
+++ b/MetaMorpheus/GUI/MainWindow.xaml
@@ -732,16 +732,19 @@
                         <Button Grid.Row="2" Grid.Column="1" Content="Create new crosslinker" 
                                 HorizontalContentAlignment="Left" BorderThickness="0" Click="AddCustomCrosslinker_Click" />
 
-                        <Button Grid.Row="4" Grid.Column="1" Content="Close program and open global settings" 
+                        <Button Grid.Row="3" Grid.Column="1" Content="Create new protease" 
+                                HorizontalContentAlignment="Left" BorderThickness="0" Click="AddCustomProtease_Click" />
+
+                        <Button Grid.Row="5" Grid.Column="1" Content="Close program and open global settings" 
                                 HorizontalContentAlignment="Left" BorderThickness="0" Click="MenuItem_OpenSettings_Click" />
 
-                        <Button Grid.Row="5" Grid.Column="1" Content="Close program and open GUI settings" 
+                        <Button Grid.Row="6" Grid.Column="1" Content="Close program and open GUI settings" 
                                 HorizontalContentAlignment="Left" BorderThickness="0" Click="MenuItem_GuiSettings_Click" />
 
-                        <Button Grid.Row="6" Grid.Column="1" Content="Open mods/data folder" 
+                        <Button Grid.Row="7" Grid.Column="1" Content="Open mods/data folder" 
                                 HorizontalContentAlignment="Left" BorderThickness="0" Click="MenuItem_OpenDataDir_Click" />
 
-                        <Button Grid.Row="7" Grid.Column="1" Content="Reset to factory defaults" 
+                        <Button Grid.Row="8" Grid.Column="1" Content="Reset to factory defaults" 
                                 HorizontalContentAlignment="Left" BorderThickness="0" Click="MenuItem_ResetDefaults_Click"
                                 ToolTip="Reset saved tasks and MetaDraw Settings to default values"/>
                     </Grid>
diff --git a/MetaMorpheus/GUI/MainWindow.xaml.cs b/MetaMorpheus/GUI/MainWindow.xaml.cs
index db8f7bd28..14716d1ac 100644
--- a/MetaMorpheus/GUI/MainWindow.xaml.cs
+++ b/MetaMorpheus/GUI/MainWindow.xaml.cs
@@ -1236,6 +1236,12 @@ private void AddCustomCrosslinker_Click(object sender, RoutedEventArgs e)
             dialog.ShowDialog();
         }
 
+        private void AddCustomProtease_Click(object sender, RoutedEventArgs e)
+        {
+            var dialog = new Views.CustomProteaseWindow();
+            dialog.ShowDialog();
+        }
+
         private void MoveTaskUp_Click(object sender, RoutedEventArgs e)
         {
             var item = GetItemDataContext(sender, e).FirstOrDefault();
diff --git a/MetaMorpheus/GUI/Views/CustomProteaseWindow.xaml b/MetaMorpheus/GUI/Views/CustomProteaseWindow.xaml
new file mode 100644
index 000000000..9e7c3391a
--- /dev/null
+++ b/MetaMorpheus/GUI/Views/CustomProteaseWindow.xaml
@@ -0,0 +1,84 @@
+<Window x:Class="MetaMorpheusGUI.Views.CustomProteaseWindow"
+        xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
+        xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+        xmlns:d="http://schemas.microsoft.com/expression/blend/2008"
+        xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
+        xmlns:local="clr-namespace:MetaMorpheusGUI.Views"
+        mc:Ignorable="d"
+        Title="CustomProteaseWindow" Height="330" Width="380" ResizeMode="NoResize" WindowStartupLocation="CenterScreen">
+    <Grid>
+        <StackPanel Orientation="Vertical" VerticalAlignment="Top" HorizontalAlignment="Center" Margin="0,5,0,0" Height="300">
+            <!--protease name-->
+            <StackPanel Orientation="Horizontal" Height="40">
+                <Label Content="Name" Width="135" Margin=" 10,5,5,5" FontSize="13"></Label>
+                <Label Content="*" Foreground="Red" FontWeight="Bold" />
+                <TextBox x:Name="ProteaseNameTextBox" Width="155" Height="25">
+                </TextBox>
+            </StackPanel>
+            <!--Cleavage specificity-->
+            <StackPanel Orientation="Horizontal" Height="40">
+                <Label Content="Cleavage Specificity" Width="135" Margin=" 10,5,5,5" Height="33" FontSize="13"></Label>
+                <Label Content="*" Foreground="Red" FontWeight="Bold" />
+                <ComboBox Name ="CleavageSpecComboBox" SelectionChanged ="CleavageSpecComboBox_SelectionChanged" Width="155" Height="25">
+                    
+                </ComboBox>
+            </StackPanel>
+            <!--Psi-MS Acession Number-->
+            <StackPanel Orientation="Horizontal" Height="40">
+                <Label Content="Psi-MS Number" Width="145" Margin=" 10,5,10,10" Height="28" FontSize="13"></Label>
+                <TextBox Name="PsiMsAccessionNumTextBox" Width="155" Height="25">
+                </TextBox>
+            </StackPanel>
+            <!--Psi-MS Name-->
+            <StackPanel Orientation="Horizontal" Height="40">
+                <Label Content="Psi-MS Name" Width="145" Margin=" 10,5,10,10" FontSize="13"></Label>
+                <TextBox Name="PsiNameTextBox" Width="155" Height="25">
+                </TextBox>
+            </StackPanel>
+            <!--Digestion motif-->
+            <StackPanel Orientation="Horizontal" Height="40">
+                <Label Content="Digestion Motif" Width="135" Margin=" 10,5,5,5" Height="31" FontSize="13"></Label>
+                <Label Content="*" Foreground="Red" FontWeight="Bold" />
+                <TextBox Name="DigestionMotifTextBox" Width="155" Height="25">
+                    <ToolTipService.ToolTip>
+                        <ToolTip Content="Amino acid sequences or motifs recognized and cleaved by the protease"/>
+                    </ToolTipService.ToolTip>
+                    <TextBox.Style>
+                        <Style TargetType="TextBox" xmlns:sys="clr-namespace:System;assembly=mscorlib">
+                            <Style.Resources>
+                                <VisualBrush x:Key="CueBannerBrush" AlignmentX="Left" AlignmentY="Center" Stretch="None">
+                                    <VisualBrush.Visual>
+                                        <Label Content="ex: 'A|', '|R', 'F[P]|'" Foreground="Gray" />
+                                    </VisualBrush.Visual>
+                                </VisualBrush>
+                            </Style.Resources>
+                            <Style.Triggers>
+                                <Trigger Property="Text" Value="{x:Static sys:String.Empty}">
+                                    <Setter Property="Background" Value="{StaticResource CueBannerBrush}" />
+                                </Trigger>
+                                <Trigger Property="Text" Value="{x:Null}">
+                                    <Setter Property="Background" Value="{StaticResource CueBannerBrush}" />
+                                </Trigger>
+                                <Trigger Property="IsKeyboardFocused" Value="True">
+                                    <Setter Property="Background" Value="White" />
+                                </Trigger>
+                            </Style.Triggers>
+                        </Style>
+                    </TextBox.Style>
+                </TextBox>
+            </StackPanel>
+            <!--Cleavage Mod-->
+            <StackPanel Orientation="Horizontal" Height="40">
+                <Label Content="Cleavage Mod" Width="145" Margin=" 10,5,10,10" Height="36" FontSize="13"></Label>
+                <TextBox Name="CleavageModTextBox" Width="155" Height="25">
+                </TextBox>
+            </StackPanel>
+            <!--Save and cancel buttons-->
+            <StackPanel Orientation="Horizontal" Height="40" HorizontalAlignment="Center"  Margin="8">
+                <Button Name="SaveProtease" Content="Save protease" FontSize="13" Margin="5" Width="100" Click="SaveProteaseButton_Click" />
+                <Button Name="CancelProtease" Content="Cancel" FontSize="13" Margin="5" Width="100" Click="CancelProteaseButton_Click" />
+            </StackPanel>
+
+        </StackPanel>
+    </Grid>
+</Window>
diff --git a/MetaMorpheus/GUI/Views/CustomProteaseWindow.xaml.cs b/MetaMorpheus/GUI/Views/CustomProteaseWindow.xaml.cs
new file mode 100644
index 000000000..40a87ed18
--- /dev/null
+++ b/MetaMorpheus/GUI/Views/CustomProteaseWindow.xaml.cs
@@ -0,0 +1,130 @@
+using Proteomics.ProteolyticDigestion;
+using System;
+using System.Collections;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using System.Windows;
+using System.Windows.Controls;
+using System.IO;
+using EngineLayer;
+using Omics.Digestion;
+using Proteomics.AminoAcidPolymer;
+
+namespace MetaMorpheusGUI.Views
+{
+    /// <summary>
+    /// Interaction logic for CustomProteaseWindow.xaml
+    /// </summary>
+    public partial class CustomProteaseWindow : Window
+    {
+        public CustomProteaseWindow()
+        {
+            InitializeComponent();
+
+            foreach (CleavageSpecificity c in Enum.GetValues(typeof(CleavageSpecificity)))
+            {
+                CleavageSpecComboBox.Items.Add(c);
+            }
+        }
+
+        private void SaveProteaseButton_Click(object sender, RoutedEventArgs e)
+        {
+            if (ProteaseNameTextBox.Text.Length == 0)
+            {
+                MessageBox.Show("Please specify the name of the protease");
+                return;
+            }
+            if (CleavageSpecComboBox.Text.Length == 0)
+            {
+                MessageBox.Show("Please specify the cleavage specificity of the protease");
+                return;
+            }
+            if (DigestionMotifTextBox.Text.Length == 0)
+            {
+                MessageBox.Show("Please specify the digestion motif(s) of the protease");
+                return;
+            }
+            string proteaseName = ProteaseNameTextBox.Text;
+            string psiMsAccessionNum = PsiMsAccessionNumTextBox.Text;
+            string psiMsName = PsiNameTextBox.Text;
+            string motifString = DigestionMotifTextBox.Text;
+
+            CleavageSpecificity cleavageSpecificity;
+            if (Enum.TryParse(CleavageSpecComboBox.Text, out CleavageSpecificity _cleaveageSpec))
+            {
+                cleavageSpecificity = _cleaveageSpec;
+            }
+            else
+            {
+                MessageBox.Show("Please specify the digestion motif(s) of the protease");
+                return;
+            }
+
+            List<DigestionMotif> digestionMotifs;
+            var aminoAcidsInMotifString = motifString.Where(char.IsLetter).ToList();
+            foreach(var aa in aminoAcidsInMotifString)
+            {
+                if (!Residue.ResiduesDictionary.ContainsKey(aa.ToString()))
+                {
+                    MessageBox.Show("Motif(s) contains invalid amino acids.");
+                    return;
+                }
+            }
+            try
+            {
+                digestionMotifs = DigestionMotif.ParseDigestionMotifsFromString(motifString);
+            }
+            catch
+            {
+                MessageBox.Show("The motif(s) could not be parsed.");
+                return;
+            }
+
+            //create a new Protease and add to ProteaseDictionary
+            Protease proteaseToAdd = new Protease(proteaseName, cleavageSpecificity, psiMsAccessionNum, psiMsName, digestionMotifs);
+
+            if (ProteaseDictionary.Dictionary.ContainsKey(proteaseName))
+            {
+                MessageBox.Show("This protease already exists");
+            }
+            else
+            {
+                if (ProteaseDictionary.Dictionary.TryAdd(proteaseName, proteaseToAdd))
+                {
+                    MessageBox.Show("Success! Protease '" + proteaseName + "' has been added to the dictionary.");
+                } 
+                else
+                {
+                    MessageBox.Show("Failed to add Protease '" + proteaseName + "' to the dictionary.");
+                }
+            }
+            
+            //customProtease file path
+            string ProtDirectory = Path.Combine(GlobalVariables.DataDir, @"ProteolyticDigestion");
+            string customProteasePath = Path.Combine(ProtDirectory, @"CustomProtease.tsv");
+
+            //check if the customProtease file exists, create it if not
+            if (!File.Exists(customProteasePath))
+            {
+                File.Create(customProteasePath);
+            }
+
+            string lineToAdd = "\n" + proteaseName + "\t" + motifString + "\t\t\t" + CleavageSpecComboBox.Text + "\t" + psiMsAccessionNum + "\t" + psiMsName + "\t\t\t\t\t";
+            var lines = new List<string> { lineToAdd };
+            File.AppendAllLines(customProteasePath, lines);
+            DialogResult = true;
+        }
+
+        private void CancelProteaseButton_Click(object sender, RoutedEventArgs e)
+        {
+            DialogResult = false;
+        }
+
+        private void CleavageSpecComboBox_SelectionChanged(object sender, SelectionChangedEventArgs e)
+        {
+
+        }
+    }
+}
diff --git a/MetaMorpheus/Test/CustomProteaseTest.cs b/MetaMorpheus/Test/CustomProteaseTest.cs
new file mode 100644
index 000000000..10029396d
--- /dev/null
+++ b/MetaMorpheus/Test/CustomProteaseTest.cs
@@ -0,0 +1,35 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using Proteomics.ProteolyticDigestion;
+using System.IO;
+using NUnit.Framework;
+using EngineLayer;
+using Omics.Digestion;
+using MzLibUtil;
+
+
+namespace Test
+{
+    public static class CustomProteaseTest
+    {
+        [Test]
+        public static void TestAddCustomProtease ()
+        {
+            string ProtDirectory = Path.Combine(GlobalVariables.DataDir, @"ProteolyticDigestion");
+            string customProteasePath = Path.Combine(ProtDirectory, @"CustomProtease.tsv");
+
+            string[] pString = new string[] { "p\tA|\t\t\tfull\tcusPsiNum\tcusPsiName\t\t\t\t\t" };
+            File.WriteAllLines(customProteasePath, pString);
+
+            GlobalVariables.LoadCustomProtease();
+            var dictionary = ProteaseDictionary.Dictionary;
+            Assert.That(ProteaseDictionary.Dictionary.ContainsKey("p"));
+            Assert.That(ProteaseDictionary.Dictionary["p"].PsiMsName == "cusPsiName");
+
+            File.Delete(customProteasePath);
+        }
+    }
+}