diff --git a/mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs b/mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs
index 067aff6d7..1b7d32d61 100644
--- a/mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs
+++ b/mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs
@@ -18,10 +18,10 @@ public class PeptideWithSetModifications : ProteolyticPeptide, IBioPolymerWithSe
     {
         public string FullSequence { get; private set; } //sequence with modifications
         public int NumFixedMods { get; }
-        // Parameter to store a hash code corresponding to a Decoy or a Target peptide
+        // Parameter to store the full sequence of the corresponding Target or Decoy peptide
         // If the peptide in question is a decoy, this pairs it to the target it was generated from
         // If the peptide in question is a target, this pairs it to its corresponding decoy 
-        public int? PairedTargetDecoyHash { get; private set; }
+        public string PairedTargetDecoySequence { get; private set; }
         /// <summary>
         /// Dictionary of modifications on the peptide. The N terminus is index 1.
         /// The key indicates which residue modification is on (with 1 being N terminus).
@@ -40,7 +40,7 @@ public class PeptideWithSetModifications : ProteolyticPeptide, IBioPolymerWithSe
         /// </summary>
         public PeptideWithSetModifications(Protein protein, IDigestionParams digestionParams, int oneBasedStartResidueInProtein,
             int oneBasedEndResidueInProtein, CleavageSpecificity cleavageSpecificity, string peptideDescription, int missedCleavages,
-           Dictionary<int, Modification> allModsOneIsNterminus, int numFixedMods, string baseSequence = null, int? pairedTargetDecoyHash = null)
+           Dictionary<int, Modification> allModsOneIsNterminus, int numFixedMods, string baseSequence = null, string pairedTargetDecoySequence = null)
            : base(protein, oneBasedStartResidueInProtein, oneBasedEndResidueInProtein, missedCleavages, cleavageSpecificity, peptideDescription, baseSequence)
         {
             _allModsOneIsNterminus = allModsOneIsNterminus;
@@ -49,7 +49,7 @@ public PeptideWithSetModifications(Protein protein, IDigestionParams digestionPa
             FullSequence = this.DetermineFullSequence();
             ProteinAccession = protein.Accession;
             UpdateCleavageSpecificity();
-            PairedTargetDecoyHash = pairedTargetDecoyHash; // Added PairedTargetDecoyHash as a nullable integer
+            PairedTargetDecoySequence = pairedTargetDecoySequence;
         }
 
         /// <summary>
@@ -59,7 +59,7 @@ public PeptideWithSetModifications(Protein protein, IDigestionParams digestionPa
         public PeptideWithSetModifications(string sequence, Dictionary<string, Modification> allKnownMods, int numFixedMods = 0,
             IDigestionParams digestionParams = null, Protein p = null, int oneBasedStartResidueInProtein = int.MinValue,
             int oneBasedEndResidueInProtein = int.MinValue, int missedCleavages = int.MinValue,
-            CleavageSpecificity cleavageSpecificity = CleavageSpecificity.Full, string peptideDescription = null, int? pairedTargetDecoyHash = null)
+            CleavageSpecificity cleavageSpecificity = CleavageSpecificity.Full, string peptideDescription = null, string pairedTargetDecoySequence = null)
             : base(p, oneBasedStartResidueInProtein, oneBasedEndResidueInProtein, missedCleavages, cleavageSpecificity, peptideDescription)
         {
             if (sequence.Contains("|"))
@@ -72,7 +72,7 @@ public PeptideWithSetModifications(string sequence, Dictionary<string, Modificat
             GetModsAfterDeserialization(allKnownMods);
             NumFixedMods = numFixedMods;
             _digestionParams = digestionParams as DigestionParams;
-            PairedTargetDecoyHash = pairedTargetDecoyHash; // Added PairedTargetDecoyHash as a nullable integer
+            PairedTargetDecoySequence = pairedTargetDecoySequence; 
 
             if (p != null)
             {
@@ -902,14 +902,7 @@ public override bool Equals(object obj)
 
         public override int GetHashCode()
         {
-            if (DigestionParams == null)
-            {
-                return FullSequence.GetHashCode();
-            }
-            else
-            {
-                return FullSequence.GetHashCode() + DigestionParams.DigestionAgent.GetHashCode();
-            }
+            return FullSequence.GetHashCode();
         }
 
         /// <summary>
@@ -1140,17 +1133,15 @@ public PeptideWithSetModifications GetReverseDecoyFromTarget(int[] revisedAminoA
             Protein decoyProtein = new Protein(proteinSequence, "DECOY_" + this.Protein.Accession, null, new List<Tuple<string, string>>(), new Dictionary<int, List<Modification>>(), null, null, null, true);
             DigestionParams d = _digestionParams;
 
-            // Creates a hash code corresponding to the target's sequence
-            int targetHash = GetHashCode();
             PeptideWithSetModifications decoyPeptide;
             //Make the "peptideDescription" store the corresponding target's sequence
             if (newBaseString != this.BaseSequence)
             {
                 decoyPeptide = new PeptideWithSetModifications(decoyProtein, d, this.OneBasedStartResidueInProtein, this.OneBasedEndResidueInProtein, this.CleavageSpecificityForFdrCategory, this.FullSequence, this.MissedCleavages, newModificationsDictionary, this.NumFixedMods, newBaseString);
                 // Sets PairedTargetDecoyHash of the original target peptie to the hash hode of the decoy sequence           
-                PairedTargetDecoyHash = decoyPeptide.GetHashCode();
+                PairedTargetDecoySequence = decoyPeptide.FullSequence;
                 // Sets PairedTargetDecoyHash of the decoy peptide to the hash code of the target sequence
-                decoyPeptide.PairedTargetDecoyHash = targetHash;
+                decoyPeptide.PairedTargetDecoySequence = this.FullSequence;
                 return decoyPeptide;
 
             }
@@ -1158,9 +1149,9 @@ public PeptideWithSetModifications GetReverseDecoyFromTarget(int[] revisedAminoA
             {
                 //The reverse decoy procedure failed to create a PeptideWithSetModificatons with a different sequence. Therefore,
                 //we retrun the mirror image peptide.
-                decoyPeptide = this.GetPeptideMirror(revisedAminoAcidOrder);
-                PairedTargetDecoyHash = decoyPeptide.GetHashCode();
-                decoyPeptide.PairedTargetDecoyHash = targetHash;
+                decoyPeptide = this.GetPeptideMirror(revisedAminoAcidOrder);       
+                PairedTargetDecoySequence = decoyPeptide.FullSequence;
+                decoyPeptide.PairedTargetDecoySequence = this.FullSequence;
                 return decoyPeptide;
             }
 
@@ -1318,17 +1309,15 @@ public PeptideWithSetModifications GetScrambledDecoyFromTarget(int[] revisedAmin
 
             Protein decoyProtein = new Protein(proteinSequence, "DECOY_" + this.Protein.Accession, null, new List<Tuple<string, string>>(), new Dictionary<int, List<Modification>>(), null, null, null, true);
             DigestionParams d = _digestionParams;
-            // Creates a hash code corresponding to the target's sequence
-            int targetHash = GetHashCode();
             PeptideWithSetModifications decoyPeptide;
             //Make the "peptideDescription" store the corresponding target's sequence
             if (newBaseString != this.BaseSequence)
             {
                 decoyPeptide = new PeptideWithSetModifications(decoyProtein, d, this.OneBasedStartResidueInProtein, this.OneBasedEndResidueInProtein, this.CleavageSpecificityForFdrCategory, this.FullSequence, this.MissedCleavages, newModificationsDictionary, this.NumFixedMods, newBaseString);
                 // Sets PairedTargetDecoyHash of the original target peptie to the hash hode of the decoy sequence           
-                PairedTargetDecoyHash = decoyPeptide.GetHashCode();
+                PairedTargetDecoySequence = decoyPeptide.FullSequence;
                 // Sets PairedTargetDecoyHash of the decoy peptide to the hash code of the target sequence
-                decoyPeptide.PairedTargetDecoyHash = targetHash;
+                decoyPeptide.PairedTargetDecoySequence = this.FullSequence;
                 return decoyPeptide;
 
             }
@@ -1337,8 +1326,8 @@ public PeptideWithSetModifications GetScrambledDecoyFromTarget(int[] revisedAmin
                 //The reverse decoy procedure failed to create a PeptideWithSetModificatons with a different sequence. Therefore,
                 //we retrun the mirror image peptide.
                 decoyPeptide = this.GetPeptideMirror(revisedAminoAcidOrder);
-                PairedTargetDecoyHash = decoyPeptide.GetHashCode();
-                decoyPeptide.PairedTargetDecoyHash = targetHash;
+                PairedTargetDecoySequence = decoyPeptide.FullSequence;
+                decoyPeptide.PairedTargetDecoySequence = this.FullSequence;
                 return decoyPeptide;
             }
         }
diff --git a/mzLib/Test/TestPeptideWithSetMods.cs b/mzLib/Test/TestPeptideWithSetMods.cs
index 4fe80b848..355d9d27c 100644
--- a/mzLib/Test/TestPeptideWithSetMods.cs
+++ b/mzLib/Test/TestPeptideWithSetMods.cs
@@ -55,7 +55,8 @@ public static void TestDifferentProteaseEquals()
             Assert.That(pep1.Parent.Equals(pep2.Parent));
             Assert.That(!pep1.DigestionParams.DigestionAgent.Equals(pep2.DigestionParams.DigestionAgent));
             Assert.That(!pep1.Equals(pep2));
-            Assert.That(!pep1.GetHashCode().Equals(pep2.GetHashCode()));
+            // HashCode is only concerned with the full sequence, not the protease. Only the equals method is interested in the protease used
+            Assert.That(pep1.GetHashCode().Equals(pep2.GetHashCode()));
         }
 
         [Test]
@@ -765,8 +766,8 @@ public static void TestReverseDecoyFromTarget()
             int testTargetHash = p.GetHashCode();
             // Hash code corresponding to the decoy sequence, should be PairedTargetDecoyHash for target
             int testDecoyHash = reverse.GetHashCode(); 
-            Assert.AreEqual(reverse.PairedTargetDecoyHash, testTargetHash);
-            Assert.AreEqual(p.PairedTargetDecoyHash, testDecoyHash);
+            Assert.AreEqual(reverse.PairedTargetDecoySequence.GetHashCode(), testTargetHash);
+            Assert.AreEqual(p.PairedTargetDecoySequence.GetHashCode(), testDecoyHash);
             Assert.AreEqual("EDITPEPK", reverse.BaseSequence);
             Assert.AreEqual(new int[] { 6, 5, 4, 3, 2, 1, 0, 7 }, newAminoAcidPositions);
             Assert.IsTrue(reverse.Protein.IsDecoy);
@@ -841,8 +842,8 @@ public static void TestReverseDecoyFromTarget()
             int testMirrorTargetHash = p_tryp.GetHashCode();
             // Hash code corresponding to the decoy sequence, should be PairedTargetDecoyHash for target
             int testMirrorDecoyHash = p_tryp_reverse.GetHashCode();
-            Assert.AreEqual(testMirrorTargetHash, p_tryp_reverse.PairedTargetDecoyHash);
-            Assert.AreEqual(testMirrorDecoyHash, p_tryp.PairedTargetDecoyHash);
+            Assert.AreEqual(testMirrorTargetHash, p_tryp_reverse.PairedTargetDecoySequence.GetHashCode());
+            Assert.AreEqual(testMirrorDecoyHash, p_tryp.PairedTargetDecoySequence.GetHashCode());
             Assert.AreEqual("RVTRITV", p_tryp_reverse.BaseSequence);
             Assert.AreEqual(new int[] { 6, 5, 4, 3, 2, 1, 0 }, newAminoAcidPositions);
             Assert.IsTrue(p_tryp_reverse.AllModsOneIsNterminus.ContainsKey(1));//n-term acetyl
@@ -871,8 +872,8 @@ public static void TestScrambledDecoyFromTarget()
             int testTargetHash = p.GetHashCode();
             // Hash code corresponding to the decoy sequence, should be PairedTargetDecoyHash for target
             int testDecoyHash = testScrambled.GetHashCode();
-            Assert.AreEqual(testScrambled.PairedTargetDecoyHash, testTargetHash);
-            Assert.AreEqual(p.PairedTargetDecoyHash, testDecoyHash);
+            Assert.AreEqual(testScrambled.PairedTargetDecoySequence.GetHashCode(), testTargetHash);
+            Assert.AreEqual(p.PairedTargetDecoySequence.GetHashCode(), testDecoyHash);
             Assert.AreEqual("IDEETPPK", testScrambled.BaseSequence);
             Assert.AreEqual(new int[] { 4, 5, 6, 1, 3, 0, 2, 7 }, newAminoAcidPositions);
             // Check n-term acetyl