diff --git a/resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql b/resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql
new file mode 100644
index 000000000..b91cbf731
--- /dev/null
+++ b/resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql
@@ -0,0 +1,13 @@
+-- Adding missing foreign keys to core.Containers(EntityId)
+ALTER TABLE targetedms.Runs ADD CONSTRAINT FK_Runs_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.QCAnnotation ADD CONSTRAINT FK_QCAnnotation_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.GuideSet ADD CONSTRAINT FK_GuideSet_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.AutoQCPing ADD CONSTRAINT FK_AutoQCPing_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.PrecursorChromInfo ADD CONSTRAINT FK_PrecursorChromInfo_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+ALTER TABLE targetedms.SampleFileChromInfo ADD CONSTRAINT FK_SampleFileChromInfo_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
+
+-- Adding missing indices on Container
+CREATE INDEX IX_QCAnnotationType_Container ON targetedms.QCAnnotationType(Container);
+CREATE INDEX IX_QCAnnotation_Container ON targetedms.QCAnnotation(Container);
+CREATE INDEX IX_GuideSet_Container ON targetedms.GuideSet(Container);
+CREATE INDEX IX_QCMetricConfiguration_Container ON targetedms.QCMetricConfiguration(Container);
diff --git a/src/org/labkey/targetedms/TargetedMSListener.java b/src/org/labkey/targetedms/TargetedMSListener.java
index dadd3c03b..7bdc6e1e3 100644
--- a/src/org/labkey/targetedms/TargetedMSListener.java
+++ b/src/org/labkey/targetedms/TargetedMSListener.java
@@ -71,5 +71,6 @@ public void containerDeleted(Container c, User user)
         new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoMSInstrument() + " WHERE Container = ?", c);
         new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoPaymentMethod() + " WHERE Container = ?", c);
         new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoRateType() + " WHERE Container = ?", c);
+        new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoSampleFileChromInfo() + " WHERE Container = ?", c);
     }
 }
diff --git a/src/org/labkey/targetedms/TargetedMSModule.java b/src/org/labkey/targetedms/TargetedMSModule.java
index 5a14f90d9..df82dd64e 100644
--- a/src/org/labkey/targetedms/TargetedMSModule.java
+++ b/src/org/labkey/targetedms/TargetedMSModule.java
@@ -231,7 +231,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 26.002;
+        return 26.004;
     }
 
     @Override