diff --git a/src/org/labkey/targetedms/SkylineDocImporter.java b/src/org/labkey/targetedms/SkylineDocImporter.java
index 6ead1941c..09c2e723e 100644
--- a/src/org/labkey/targetedms/SkylineDocImporter.java
+++ b/src/org/labkey/targetedms/SkylineDocImporter.java
@@ -1404,7 +1404,7 @@ private Map<String, Set<String>> getIdentifiers(ProteinService proteinService, P
         Set<String> skylineIdentifiers = new HashSet<>();
         if(label != null)
         {
-            // prot.identifers table limits the name to 50 characters
+            // prot.identifiers table limits the name to 50 characters
             skylineIdentifiers.add(label.substring(0, Math.min(50, label.length())));
         }
         if(name != null)
diff --git a/src/org/labkey/targetedms/TargetedMSSchema.java b/src/org/labkey/targetedms/TargetedMSSchema.java
index 852f79df9..8865bee43 100644
--- a/src/org/labkey/targetedms/TargetedMSSchema.java
+++ b/src/org/labkey/targetedms/TargetedMSSchema.java
@@ -722,7 +722,8 @@ public List<AnnotatedTargetedMSTable.AnnotationSettingForTyping> getAnnotationSe
                     "Targets " +
                     "  FROM ");
             annoSettingsSql.append(annotationSettingsTI, " annoSettings ");
-            annoSettingsSql.append(" INNER JOIN ").append(TargetedMSManager.getTableInfoRuns(), " runs ON runs.Id = annoSettings.RunId");
+            annoSettingsSql.append(" INNER JOIN ").append(TargetedMSManager.getTableInfoRuns(), "runs");
+            annoSettingsSql.append(" ON runs.Id = annoSettings.RunId");
             annoSettingsSql.append(" WHERE ");
             annoSettingsSql.append(containerFilter.getSQLFragment(getDbSchema(), new SQLFragment("runs.Container")));
             // AnnotationSettings table has a "Targets" column that determines which targets
diff --git a/src/org/labkey/targetedms/datasource/MsDataSourceTypes.java b/src/org/labkey/targetedms/datasource/MsDataSourceTypes.java
index b903d5e07..64d847f11 100644
--- a/src/org/labkey/targetedms/datasource/MsDataSourceTypes.java
+++ b/src/org/labkey/targetedms/datasource/MsDataSourceTypes.java
@@ -50,8 +50,8 @@ public SimpleFilter.FilterClause getDirContentsFilterClause()
                 public SQLFragment toSQLFragment(Map<FieldKey, ? extends ColumnInfo> columnMap, SqlDialect dialect)
                 {
                     ColumnInfo colInfo = columnMap != null ? columnMap.get(getFieldKey()) : null;
-                    String alias = colInfo != null ? colInfo.getAlias() : getFieldKey().getName();
-                    return new SQLFragment(dialect.getColumnSelectName(alias))
+                    var alias = SimpleFilter.getAliasForColumnFilter(dialect,colInfo, getFieldKey());
+                    return new SQLFragment().appendIdentifier(alias)
                             .append(" ").append(dialect.getCaseInsensitiveLikeOperator()).append(" ? ")
                             .append(sqlEscape())
                             .add(escapeLikePattern("_") + "FUNC%.DAT");
diff --git a/src/org/labkey/targetedms/query/SkylineAuditTable.java b/src/org/labkey/targetedms/query/SkylineAuditTable.java
index 73c44dec4..955deaad7 100644
--- a/src/org/labkey/targetedms/query/SkylineAuditTable.java
+++ b/src/org/labkey/targetedms/query/SkylineAuditTable.java
@@ -92,7 +92,7 @@ public SkylineAuditTable(@NotNull String name, @NotNull TargetedMSSchema schema,
         cteSQL.add(_run.getDocumentGUID());
 
         SQLFragment result = new SQLFragment();
-        result.addCommonTableExpression("TargetedMSAuditCTE", "logTree", cteSQL, getSqlDialect().isPostgreSQL());
+        result.addCommonTableExpression(getSqlDialect(), "TargetedMSAuditCTE", "logTree", cteSQL, getSqlDialect().isPostgreSQL());
         result.append("SELECT lt.* \n");
 
         result.append(", CASE WHEN msg.orderNumber = 0 AND lt.extraInfo IS NOT NULL THEN '(info)' END AS HasExtraInfo\n");
diff --git a/src/org/labkey/targetedms/query/SkylineListUnionTable.java b/src/org/labkey/targetedms/query/SkylineListUnionTable.java
index 59b45fd4e..c658f5856 100644
--- a/src/org/labkey/targetedms/query/SkylineListUnionTable.java
+++ b/src/org/labkey/targetedms/query/SkylineListUnionTable.java
@@ -40,7 +40,7 @@ public SkylineListUnionTable(SkylineListSchema schema, SkylineListTable listTabl
 
         for (ColumnInfo childColumn : listTable.getColumns())
         {
-            BaseColumnInfo column = new ExprColumn(this, childColumn.getFieldKey(), new SQLFragment(ExprColumn.STR_TABLE_ALIAS + " ." + childColumn.getAlias()), childColumn.getJdbcType());
+            BaseColumnInfo column = new ExprColumn(this, childColumn.getFieldKey(), new SQLFragment().appendDottedIdentifiers(ExprColumn.STR_TABLE_ALIAS,childColumn.getAlias()), childColumn.getJdbcType());
             column.setKeyField(childColumn.isKeyField());
             addColumn(column);
         }
@@ -74,7 +74,7 @@ public SkylineListUnionTable(SkylineListSchema schema, SkylineListTable listTabl
                 result.append(",\n ");
                 result.append(colInfo.getValueSql(innerAlias));
                 result.append(" AS ");
-                result.appendIdentifier(getSqlDialect().makeLegalIdentifier(colInfo.getAlias()));
+                result.appendIdentifier(colInfo.getAlias());
             }
             result.append(" FROM ");
             result.append(table.getFromSQL(innerAlias));
diff --git a/webapp/TargetedMS/js/QCPlotLegendHelper.js b/webapp/TargetedMS/js/QCPlotLegendHelper.js
index 5de6755e9..8c7dc3511 100644
--- a/webapp/TargetedMS/js/QCPlotLegendHelper.js
+++ b/webapp/TargetedMS/js/QCPlotLegendHelper.js
@@ -146,7 +146,7 @@ if (!LABKEY.targetedms.QCPlotLegendHelper) {
             var suffix = this.getSuffix(identifier);
             var matchingPrefixAndSuffix = matchingPrefixes[suffix];
 
-            // If there is only one sequence with this prefix, return the prefix (unless the identifer is already short enough).
+            // If there is only one sequence with this prefix, return the prefix (unless the identifier is already short enough).
             if (Object.keys(matchingPrefixes).length === 1 && Object.keys(matchingPrefixAndSuffix).length === 1)
                 return this.shorterOf((identifier.length > (this.minLegendLength * 2) + 1) ? (prefix + this.ellipsis) : identifier, identifier);