diff --git a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsAlignmentRefiner.cs b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsAlignmentRefiner.cs
index 03127cc4d..ca117ec18 100644
--- a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsAlignmentRefiner.cs
+++ b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsAlignmentRefiner.cs
@@ -19,10 +19,10 @@ protected override List<AlignmentSpotProperty> GetCleanedSpots(List<AlignmentSpo
             if (!(_param is MsdialGcmsParameter param)) return alignmentSpotList;
 
             var cSpots = new List<AlignmentSpotProperty>();
-            cSpots.AddRange(alignmentSpotList.Where(spot => spot.IsReferenceMatched(evaluator)));
+            cSpots.AddRange(alignmentSpotList.Where(spot => spot.IsReferenceMatched(evaluator) && !spot.Name.StartsWith("Putative")));
 
             //if both Quant mass and Retention is same, exclude the spot information.
-            foreach (var aSpot in alignmentSpotList.Where(spot => !spot.IsReferenceMatched(evaluator))) {
+            foreach (var aSpot in alignmentSpotList.Where(spot => !spot.IsReferenceMatched(evaluator) || spot.Name.StartsWith("Putative"))) {
                 var aSpotRt = aSpot.TimesCenter.RT.Value;
                 var aSpotRi = aSpot.TimesCenter.RI.Value;
                 var aSpotMass = aSpot.QuantMass;
diff --git a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs
index 1c516b44c..19660d59b 100644
--- a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs
+++ b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsPeakJoiner.cs
@@ -137,7 +137,7 @@ private bool QuantMassExists(double quantMass, MSDecResult result) {
 
     protected bool IsSimilarTo(SpectrumFeature x, SpectrumFeature y) {
         var result = MsScanMatching.CompareEIMSScanProperties(x.AnnotatedMSDecResult.MSDecResult, y.AnnotatedMSDecResult.MSDecResult, _msMatchParam,
-            _alignmentParameter.Ms1AlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance, 
+            _alignmentParameter.Ms1AlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance, _parameter.RetentionIndexAlignmentTolerance, 
             _alignmentParameter.Ms1AlignmentFactor, _alignmentParameter.RetentionTimeAlignmentFactor, _indextype == AlignmentIndexType.RI);
         var isRetentionMatch = _indextype == AlignmentIndexType.RI ? result.IsRiMatch : result.IsRtMatch;
         return result.IsSpectrumMatch && isRetentionMatch;
@@ -145,7 +145,7 @@ protected bool IsSimilarTo(SpectrumFeature x, SpectrumFeature y) {
 
     protected double GetSimilality(SpectrumFeature x, SpectrumFeature y) {
         var result = MsScanMatching.CompareEIMSScanProperties(x.AnnotatedMSDecResult.MSDecResult, y.AnnotatedMSDecResult.MSDecResult, _msMatchParam,
-            _alignmentParameter.Ms1AlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance,
+            _alignmentParameter.Ms1AlignmentTolerance, _alignmentParameter.RetentionTimeAlignmentTolerance, _parameter.RetentionIndexAlignmentTolerance,
             _alignmentParameter.Ms1AlignmentFactor, _alignmentParameter.RetentionTimeAlignmentFactor, _indextype == AlignmentIndexType.RI);
         return result.TotalScore;
     }