diff --git a/protein/api-src/org/labkey/api/protein/go/GoLoader.java b/protein/api-src/org/labkey/api/protein/go/GoLoader.java
index 9f6b95c8c7..cd39db1fe5 100644
--- a/protein/api-src/org/labkey/api/protein/go/GoLoader.java
+++ b/protein/api-src/org/labkey/api/protein/go/GoLoader.java
@@ -143,14 +143,25 @@ public void load()
         });
     }
 
-    private void loadGoFromGz() throws SQLException, IOException, ServletException
+    public static void dropGoIndexes()
     {
         DbSchema schema = ProteinSchema.getSchema();
+        new SqlExecutor(schema).execute(schema.getSqlDialect().execute(schema, "drop_go_indexes", ""));
+    }
+
+    public static void createGoIndexes()
+    {
+        DbSchema schema = ProteinSchema.getSchema();
+        new SqlExecutor(schema).execute(schema.getSqlDialect().execute(schema, "create_go_indexes", ""));
+    }
+
+    private void loadGoFromGz() throws SQLException, IOException, ServletException
+    {
         Map<String, GoLoadBean> map = getGoLoadMap();
         long start = System.currentTimeMillis();
 
         clearGoLoaded();
-        new SqlExecutor(schema).execute(schema.getSqlDialect().execute(schema, "drop_go_indexes", ""));
+        dropGoIndexes();
 
         logStatus("Starting to load GO annotation files");
         logStatus("");
@@ -175,7 +186,7 @@ private void loadGoFromGz() throws SQLException, IOException, ServletException
             }
         }
 
-        new SqlExecutor(schema).execute(schema.getSqlDialect().execute(schema, "create_go_indexes", ""));
+        createGoIndexes();
         long elapsed = System.currentTimeMillis() - start;
 
         logStatus("Successfully loaded all GO annotation files (" + DateUtil.formatDuration(elapsed) + ")");
diff --git a/protein/src/org/labkey/protein/ProteinModule.java b/protein/src/org/labkey/protein/ProteinModule.java
index d17e618e72..fd9d076f5c 100644
--- a/protein/src/org/labkey/protein/ProteinModule.java
+++ b/protein/src/org/labkey/protein/ProteinModule.java
@@ -22,8 +22,8 @@
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.DatabaseMigrationService;
 import org.labkey.api.data.DatabaseMigrationService.DefaultMigrationHandler;
-import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.SqlExecutor;
+import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.files.FileContentService;
 import org.labkey.api.files.TableUpdaterFileListener;
@@ -36,9 +36,11 @@
 import org.labkey.api.protein.annotation.CustomAnnotationSetManager;
 import org.labkey.api.protein.annotation.ProteinAnnotationPipelineProvider;
 import org.labkey.api.protein.fasta.FastaDbLoader;
+import org.labkey.api.protein.go.GoLoader;
 import org.labkey.api.protein.query.CustomAnnotationSchema;
 import org.labkey.api.protein.query.ProteinUserSchema;
 import org.labkey.api.protein.search.MSSearchWebpart;
+import org.labkey.api.query.FieldKey;
 import org.labkey.api.usageMetrics.UsageMetricsService;
 import org.labkey.api.view.BaseWebPartFactory;
 import org.labkey.api.view.Portal;
@@ -129,18 +131,30 @@ public void doStartup(ModuleContext moduleContext)
         }
 
         ProteinService.get().registerProteinSearchView(new ProteinSearchViewProvider());
-        DatabaseMigrationService.get().registerHandler(ProteinSchema.getSchema(), new DefaultMigrationHandler()
+        DatabaseMigrationService.get().registerHandler(new DefaultMigrationHandler(ProteinSchema.getSchema())
         {
             @Override
-            public void beforeSchema(DbSchema targetSchema)
+            public void beforeSchema()
             {
-                new SqlExecutor(targetSchema).execute("ALTER TABLE prot.Organisms DROP CONSTRAINT FK_ProtOrganisms_ProtIdentifiers");
+                new SqlExecutor(getSchema()).execute("ALTER TABLE prot.Organisms DROP CONSTRAINT FK_ProtOrganisms_ProtIdentifiers");
+                GoLoader.dropGoIndexes();
             }
 
             @Override
-            public void afterSchema(DbSchema targetSchema)
+            public @Nullable FieldKey getContainerFieldKey(TableInfo sourceTable)
             {
-                new SqlExecutor(targetSchema).execute("ALTER TABLE prot.Organisms ADD CONSTRAINT FK_ProtOrganisms_ProtIdentifiers FOREIGN KEY (IdentId) REFERENCES prot.Identifiers (IdentId)");
+                return switch (sourceTable.getName())
+                {
+                    case "CustomAnnotation", "CustomAnnotationSet" -> super.getContainerFieldKey(sourceTable);
+                    default -> SITE_WIDE_TABLE;
+                };
+            }
+
+            @Override
+            public void afterSchema()
+            {
+                new SqlExecutor(getSchema()).execute("ALTER TABLE prot.Organisms ADD CONSTRAINT FK_ProtOrganisms_ProtIdentifiers FOREIGN KEY (IdentId) REFERENCES prot.Identifiers (IdentId)");
+                GoLoader.createGoIndexes();
             }
         });
     }