smith-chem-wisc · trishorts · Nov 18, 2021 · Nov 18, 2021 · Feb 4, 2022 · Feb 15, 2022
diff --git a/mzLib/MassSpectrometry/MzSpectra/SpectralSimilarity.cs b/mzLib/MassSpectrometry/MzSpectra/SpectralSimilarity.cs
@@ -160,7 +160,10 @@ private double[] Normalize(double[] spectrum, SpectrumNormalizationScheme scheme
                 if (index > 0)
                 {
                     //didn't find a experimental mz in range
-                    intensityPairs.Add((0, xyPair.Item2));
+                    if (allPeaks)
+                    {
+                        intensityPairs.Add((0, xyPair.Item2));
+                    }
                 }
             }
 
@@ -172,6 +175,11 @@ private double[] Normalize(double[] spectrum, SpectrumNormalizationScheme scheme
                     intensityPairs.Add((xyPair.Item2, 0));
                 }
             }
+
+            if (intensityPairs.Count == 0)
+            {
+                intensityPairs.Add((-1, -1));
+            }
             return intensityPairs;
         }