diff --git a/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java b/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java
index 707128d44..73d10893e 100644
--- a/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java
+++ b/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java
@@ -24,7 +24,6 @@ public class QCMetricConfiguration implements Comparable<QCMetricConfiguration>
     private String _name;
     private String _queryName;
     private boolean _precursorScoped;
-    private String _enabledQueryName;
     private QCMetricStatus _status;
     private String _traceName;
     private Double _minTimeValue;
@@ -75,16 +74,6 @@ public void setPrecursorScoped(boolean precursorScoped)
         _precursorScoped = precursorScoped;
     }
 
-    public String getEnabledQueryName()
-    {
-        return _enabledQueryName;
-    }
-
-    public void setEnabledQueryName(String enabledQueryName)
-    {
-        _enabledQueryName = enabledQueryName;
-    }
-
     public QCMetricStatus getStatus()
     {
         return _status;
@@ -182,9 +171,6 @@ public JSONObject toJSON(){
         jsonObject.put("queryName", _queryName);
         jsonObject.put("precursorScoped",  _precursorScoped);
         jsonObject.put("metricStatus", getStatus() == null ? QCMetricStatus.DEFAULT.toString() : getStatus().toString());
-        if (_enabledQueryName != null) {
-            jsonObject.put("enabledQueryName", _enabledQueryName);
-        }
         if (_traceName != null) {
             jsonObject.put("traceName", _traceName);
         }
diff --git a/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorAccuracy.sql b/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorAccuracy.sql
deleted file mode 100644
index f35643bdb..000000000
--- a/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorAccuracy.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT 1 AS E WHERE EXISTS (SELECT Id FROM targetedms.PrecursorChromInfoAnnotation WHERE Name = 'PrecursorAccuracy')
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorLOD.sql b/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorLOD.sql
deleted file mode 100644
index 65dcf6b0a..000000000
--- a/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorLOD.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT 1 AS E WHERE EXISTS (SELECT Id FROM targetedms.PrecursorChromInfoAnnotation WHERE Name = 'LOD')
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorLOQ.sql b/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorLOQ.sql
deleted file mode 100644
index c49c4f0f7..000000000
--- a/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorLOQ.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT 1 AS E WHERE EXISTS (SELECT Id FROM targetedms.PrecursorChromInfoAnnotation WHERE Name = 'LOQ')
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorRSquared.sql b/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorRSquared.sql
deleted file mode 100644
index a392b3fc4..000000000
--- a/resources/queries/targetedms/QCMetricEnabled_IsotopologuePrecursorRSquared.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT 1 AS E WHERE EXISTS (SELECT Id FROM targetedms.PrecursorChromInfoAnnotation WHERE Name = 'RSquared')
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetricEnabled_isotopeDotp.sql b/resources/queries/targetedms/QCMetricEnabled_isotopeDotp.sql
deleted file mode 100644
index 1fbdec14c..000000000
--- a/resources/queries/targetedms/QCMetricEnabled_isotopeDotp.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT 1 AS E WHERE EXISTS (SELECT Id FROM targetedms.PrecursorChromInfo WHERE IsotopeDotp IS NOT NULL)
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetricEnabled_lhRatio.sql b/resources/queries/targetedms/QCMetricEnabled_lhRatio.sql
deleted file mode 100644
index dfa290189..000000000
--- a/resources/queries/targetedms/QCMetricEnabled_lhRatio.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT 1 AS E WHERE EXISTS (SELECT Id FROM targetedms.PrecursorAreaRatio)
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetricEnabled_libraryDotp.sql b/resources/queries/targetedms/QCMetricEnabled_libraryDotp.sql
deleted file mode 100644
index 47cb1422f..000000000
--- a/resources/queries/targetedms/QCMetricEnabled_libraryDotp.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT 1 AS E WHERE EXISTS (SELECT Id FROM targetedms.PrecursorChromInfo WHERE LibraryDotp IS NOT NULL)
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetricEnabled_massErrorPrecursor.sql b/resources/queries/targetedms/QCMetricEnabled_massErrorPrecursor.sql
deleted file mode 100644
index 4b935593a..000000000
--- a/resources/queries/targetedms/QCMetricEnabled_massErrorPrecursor.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT 1 AS E WHERE EXISTS (SELECT Id FROM targetedms.TransitionChromInfo WHERE MassErrorPPM IS NOT NULL AND TransitionId.Charge IS NULL)
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetricEnabled_massErrorTransition.sql b/resources/queries/targetedms/QCMetricEnabled_massErrorTransition.sql
deleted file mode 100644
index 9fa98891e..000000000
--- a/resources/queries/targetedms/QCMetricEnabled_massErrorTransition.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT 1 AS E WHERE EXISTS (SELECT Id FROM targetedms.TransitionChromInfo WHERE MassErrorPPM IS NOT NULL AND TransitionId.Charge IS NOT NULL)
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetricEnabled_precursorAndTransitionAreas.sql b/resources/queries/targetedms/QCMetricEnabled_precursorAndTransitionAreas.sql
deleted file mode 100644
index 0705cc577..000000000
--- a/resources/queries/targetedms/QCMetricEnabled_precursorAndTransitionAreas.sql
+++ /dev/null
@@ -1,20 +0,0 @@
-/*
- * Copyright (c) 2016-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
--- We need both transition and precursor areas
-SELECT 1 AS E
-WHERE
-    EXISTS (SELECT E FROM QCMetricEnabled_precursorArea)
-    AND EXISTS (SELECT E FROM QCMetricEnabled_transitionArea)
diff --git a/resources/queries/targetedms/QCMetric_massErrorTransition.sql b/resources/queries/targetedms/QCMetric_massErrorTransition.sql
index ba627d5ce..20127dc67 100644
--- a/resources/queries/targetedms/QCMetric_massErrorTransition.sql
+++ b/resources/queries/targetedms/QCMetric_massErrorTransition.sql
@@ -18,7 +18,7 @@ SELECT * FROM (
                       pci.Id AS PrecursorChromInfoId,
                       SampleFileId AS SampleFileId,
                       -- Use the error from the most intense transition associated with the precursor
-                      (SELECT COALESCE(MassErrorPPM, -1000) AS MetricValue
+                      (SELECT COALESCE(MassErrorPPM, -100000) AS MetricValue
                        FROM TransitionChromInfo tci
                        WHERE TransitionId.Charge IS NOT NULL
                          AND tci.PrecursorChromInfoId = pci.Id
@@ -26,3 +26,4 @@ SELECT * FROM (
                        ORDER BY Area DESC, Id LIMIT 1) AS MetricValue FROM PrecursorChromInfo pci
  ) X
 WHERE MetricValue IS NOT NULL
+AND MetricValue != -100000
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetric_peakArea.sql b/resources/queries/targetedms/QCMetric_peakArea.sql
index f131b6931..0244e9302 100644
--- a/resources/queries/targetedms/QCMetric_peakArea.sql
+++ b/resources/queries/targetedms/QCMetric_peakArea.sql
@@ -17,4 +17,9 @@ SELECT
   Id AS PrecursorChromInfoId,
   SampleFileId AS SampleFileId,
   TotalArea AS MetricValue
-FROM PrecursorChromInfo
\ No newline at end of file
+FROM PrecursorChromInfo
+WHERE
+    -- Ensure we have precursor areas for peptides or small molecules
+    EXISTS (SELECT * FROM QCMetricEnabled_precursorArea)
+    -- Ensure we have transition areas for peptides or small molecules
+    AND EXISTS (SELECT * FROM QCMetricEnabled_transitionArea)
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetric_precursorArea.sql b/resources/queries/targetedms/QCMetric_precursorArea.sql
index 008b1c536..38b866020 100644
--- a/resources/queries/targetedms/QCMetric_precursorArea.sql
+++ b/resources/queries/targetedms/QCMetric_precursorArea.sql
@@ -14,7 +14,9 @@
  * limitations under the License.
  */
 SELECT
-  Id AS PrecursorChromInfoId,
-  SampleFileId AS SampleFileId,
-  TotalPrecursorArea AS MetricValue
-FROM PrecursorChromInfo
\ No newline at end of file
+    Id AS PrecursorChromInfoId,
+    SampleFileId AS SampleFileId,
+    TotalPrecursorArea AS MetricValue
+FROM PrecursorChromInfo
+WHERE
+    EXISTS (SELECT * FROM QCMetricEnabled_precursorArea)
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCMetric_transitionArea.sql b/resources/queries/targetedms/QCMetric_transitionArea.sql
index 0629c06ab..9eb7d8d70 100644
--- a/resources/queries/targetedms/QCMetric_transitionArea.sql
+++ b/resources/queries/targetedms/QCMetric_transitionArea.sql
@@ -17,4 +17,6 @@ SELECT
   Id AS PrecursorChromInfoId,
   SampleFileId AS SampleFileId,
   TotalNonPrecursorArea AS MetricValue
-FROM PrecursorChromInfo
\ No newline at end of file
+FROM PrecursorChromInfo
+WHERE
+  EXISTS (SELECT * FROM QCMetricEnabled_transitionArea)
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCRunMetricEnabled_iRTCorrelation.sql b/resources/queries/targetedms/QCRunMetricEnabled_iRTCorrelation.sql
deleted file mode 100644
index 0b3d07909..000000000
--- a/resources/queries/targetedms/QCRunMetricEnabled_iRTCorrelation.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT Id FROM targetedms.SampleFile WHERE IRTCorrelation IS NOT NULL
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCRunMetricEnabled_iRTIntercept.sql b/resources/queries/targetedms/QCRunMetricEnabled_iRTIntercept.sql
deleted file mode 100644
index 0512c072f..000000000
--- a/resources/queries/targetedms/QCRunMetricEnabled_iRTIntercept.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT Id FROM targetedms.SampleFile WHERE IRTIntercept IS NOT NULL
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCRunMetricEnabled_iRTSlope.sql b/resources/queries/targetedms/QCRunMetricEnabled_iRTSlope.sql
deleted file mode 100644
index 9a6aa8440..000000000
--- a/resources/queries/targetedms/QCRunMetricEnabled_iRTSlope.sql
+++ /dev/null
@@ -1 +0,0 @@
-SELECT Id FROM targetedms.SampleFile WHERE IRTSlope IS NOT NULL
\ No newline at end of file
diff --git a/resources/queries/targetedms/QCRunMetricEnabled_ticArea.sql b/resources/queries/targetedms/QCRunMetricEnabled_ticArea.sql
deleted file mode 100644
index 68a4ebb49..000000000
--- a/resources/queries/targetedms/QCRunMetricEnabled_ticArea.sql
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * Copyright (c) 2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-SELECT Id FROM targetedms.SampleFile WHERE TicArea IS NOT NULL
diff --git a/resources/queries/targetedms/qcMetricsConfig.sql b/resources/queries/targetedms/qcMetricsConfig.sql
index 2a4ff616d..d1f1248ef 100644
--- a/resources/queries/targetedms/qcMetricsConfig.sql
+++ b/resources/queries/targetedms/qcMetricsConfig.sql
@@ -20,7 +20,6 @@ SELECT
        qmc.QueryName,
        qmc.PrecursorScoped,
        qmc.Container, -- including to lock out editing pre-configured qc metrics,
-       qmc.EnabledQueryName,
        qem.Status,
        CASE WHEN qem.metric IS NULL THEN FALSE
             ELSE TRUE END AS Inserted,
diff --git a/resources/schemas/dbscripts/postgresql/targetedms-25.005-25.006.sql b/resources/schemas/dbscripts/postgresql/targetedms-25.005-25.006.sql
new file mode 100644
index 000000000..4e7d0a41d
--- /dev/null
+++ b/resources/schemas/dbscripts/postgresql/targetedms-25.005-25.006.sql
@@ -0,0 +1,21 @@
+CREATE TABLE targetedms.QCMetricCache
+(
+    Container       entityid NOT NULL,
+    MetricId        INT NOT NULL,
+    PrecursorChromInfoId BIGINT,
+    SampleFileId    BIGINT NOT NULL,
+    MetricValue     REAL,
+    SeriesLabel     VARCHAR(200),
+
+    CONSTRAINT PK_QCMetricCache PRIMARY KEY (Container, MetricId, PrecursorChromInfoId),
+    CONSTRAINT FK_QCMetricCache_PrecursorChromInfoId FOREIGN KEY (PrecursorChromInfoId) REFERENCES targetedms.PrecursorChromInfo(Id),
+    CONSTRAINT FK_QCMetricCache_SampleFileId FOREIGN KEY (SampleFileId) REFERENCES targetedms.SampleFile(Id),
+    CONSTRAINT FK_QCMetricCache_MetricIdId FOREIGN KEY (MetricId) REFERENCES targetedms.QCMetricConfiguration(Id),
+    CONSTRAINT FK_QCMetricCache_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId)
+);
+
+CREATE INDEX IDX_QCMetricCache_PrecursorChromInfoId ON targetedms.QCMetricCache(PrecursorChromInfoId);
+CREATE INDEX IDX_QCMetricCache_SampleFileId ON targetedms.QCMetricCache(SampleFileId);
+CREATE INDEX IDX_QCMetricCache_MetricId ON targetedms.QCMetricCache(MetricId);
+
+ALTER TABLE targetedms.QCMetricConfiguration DROP COLUMN EnabledQueryName;
\ No newline at end of file
diff --git a/resources/schemas/targetedms.xml b/resources/schemas/targetedms.xml
index fac2bdef5..ab3cba8e1 100644
--- a/resources/schemas/targetedms.xml
+++ b/resources/schemas/targetedms.xml
@@ -1349,7 +1349,6 @@
             <column columnName="Name"/>
             <column columnName="QueryName"/>
             <column columnName="PrecursorScoped"/>
-            <column columnName="EnabledQueryName"/>
             <column columnName="TraceValue"/>
             <column columnName="MinTimeValue"/>
             <column columnName="MaxTimeValue"/>
@@ -1940,4 +1939,14 @@
             <column columnName="Nickname"/>
         </columns>
     </table>
+    <table tableName="QCMetricCache" tableDbType="TABLE">
+        <columns>
+            <column columnName="Container"/>
+            <column columnName="MetricId"/>
+            <column columnName="PrecursorChromInfoId"/>
+            <column columnName="SampleFileId"/>
+            <column columnName="MetricValue"/>
+            <column columnName="SeriesLabel"/>
+        </columns>
+    </table>
 </tables>
diff --git a/resources/views/configureQCMetric.html b/resources/views/configureQCMetric.html
index d0880f74f..9a608a2c5 100644
--- a/resources/views/configureQCMetric.html
+++ b/resources/views/configureQCMetric.html
@@ -4,7 +4,8 @@
 </p>
 
 <div id="qcMetricsTable">Loading...</div>
-<div id="qcMetricsError"></div>
+<div id="qcMetricsError" class="labkey-error"></div>
+<div id="linkToRawTable"></div>
 <script type="text/javascript" nonce="<%=scriptNonce%>">
 
     if (!LABKEY.internal)
@@ -28,9 +29,9 @@
                                 '</tr>';
 
             jQuery.each(qcMetrics, function (index, row) {
-                var rowClass = index % 2 === 1 ? "labkey-row" : "labkey-alternate-row";
+                const rowClass = index % 2 === 1 ? "labkey-row" : "labkey-alternate-row";
                 configRows.push({metric: row.id, name: row.name, Status: row.Status, Inserted: row.Inserted});
-                var editLock = row.Container === LABKEY.container.id;
+                const editLock = row.Container === LABKEY.container.id;
 
                 qcMetricsTable += '<tr class="' + rowClass + '">';
 
@@ -57,12 +58,13 @@
                 qcMetricsTable += '</tr>';
             });
 
-            qcMetricsTable += '</table>' + '<br>' +
+            qcMetricsTable += '</table><br>' +
                     '<button type="button" class="labkey-button primary" id="saveButton" style="margin-right: 20px;">Save</button>' +
                     '<button type="button" class="labkey-button" id="cancelButton" style="margin-right: 20px;">Cancel</button>' +
                     '<button type="button" class="labkey-button" id="createNewCustomMetricButton" style="margin-right: 20px;">Add New Custom Metric</button>' +
-                    '<button type="button" class="labkey-button" id="createNewTraceMetricButton">Add New Trace Metric</button>' +
-                    '</form>';
+                    '<button type="button" class="labkey-button" id="createNewTraceMetricButton" style="margin-right: 20px;">Add New Trace Metric</button>' +
+                    '<button type="button" class="labkey-button" id="clearCacheButton">Clear Cached Metric Values</button>' +
+                    '</form><br>Edits to queries backing existing custom metrics require a manual cache clearing to display the updated results.</p>';
 
             jQuery('#qcMetricsTable').html(qcMetricsTable);
 
@@ -80,6 +82,17 @@
             jQuery('#createNewTraceMetricButton').click(function() {
                 LABKEY.internal.ConfigureQCMetrics.addNewMetric('trace')
             });
+            jQuery('#clearCacheButton').click(function() {
+                jQuery('#qcMetricsError').text('Clearing cached metrics...');
+                LABKEY.Ajax.request({
+                    url: LABKEY.ActionURL.buildURL('targetedms', 'clearQCMetricsCache.api'),
+                    method: 'POST',
+                    success: function() {
+                        jQuery('#qcMetricsError').text('Cleared cached metrics.');
+                    },
+                    failure: LABKEY.Utils.getCallbackWrapper(LABKEY.internal.ConfigureQCMetrics.onError, this, true)
+                });
+            });
 
             jQuery.each(qcMetrics, function (index, row) {
                 jQuery('#editLink' + row.id).click(function (e) {
@@ -87,7 +100,7 @@
                     LABKEY.internal.ConfigureQCMetrics.editMetric(jQuery('#editLink' + row.id).text());
                     return false;
                 });
-                jQuery('#select-' + row.id).change(function (e) {
+                jQuery('#select-' + row.id).change(function () {
                     refreshBoundsInputs(qcMetrics);
                 });
             });
@@ -103,7 +116,7 @@
         }
 
         function getReturnUrl() {
-            var returnUrl = LABKEY.ActionURL.getParameter('returnUrl');
+            const returnUrl = LABKEY.ActionURL.getParameter('returnUrl');
 
             if(returnUrl) {
                 return returnUrl;
@@ -125,30 +138,36 @@
                         qcMetrics = result.rows;
                         showQCMetrics();
                     },
-                    failure: LABKEY.Utils.getCallbackWrapper(LABKEY.internal.ConfigureQCMetrics.onError, this, true)
+                    failure: LABKEY.Utils.getCallbackWrapper(LABKEY.internal.ConfigureQCMetrics.onErrorClearLoading, this, true)
                 });
             },
 
+            onErrorClearLoading: function(exception, responseObj, response2){
+                this.onError(exception, responseObj, response2);
+                jQuery('#qcMetricsTable').text('');
+            },
+
             onError: function(exception, responseObj, response2){
                 console.error(arguments);
 
-                var msg = LABKEY.Utils.getMsgFromError(response2, exception, {
+                const msg = LABKEY.Utils.getMsgFromError(response2, exception, {
                     showExceptionClass: false,
                     msgPrefix: 'Error: '
                 });
 
                 jQuery('#qcMetricsError').text(msg);
+                jQuery('#linkToRawTable').html(LABKEY.Utils.textLink({href: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'targetedms', queryName: 'QCMetricConfiguration'}), text: 'View QC metrics table'}));
             },
 
             editMetric: function (metricName) {
-                var clickedQcMetricConfig = {};
+                let clickedQcMetricConfig = {};
                 jQuery.each(qcMetrics, function (index, row) {
                     if (row.name === metricName) {
                         clickedQcMetricConfig = row;
                     }
                 });
 
-                var op = 'update';
+                const op = 'update';
                 if (clickedQcMetricConfig.TraceName) {
                     LABKEY.internal.ConfigureQCMetrics.showTraceMetricWindow(op, clickedQcMetricConfig)
                 }
@@ -166,7 +185,7 @@
                     scope: this,
                     containerPath: LABKEY.container.id,
                     success:  function(schemasInfo) {
-                        var windowConfig = {
+                        const windowConfig = {
                             parent: this,
                             schemas: schemasInfo.schemas,
                             operation: op
@@ -188,17 +207,18 @@
                     filterArray: [LABKEY.Filter.create('TextId', null, LABKEY.Filter.Types.NOT_MISSING)],
                     success: function (sampleFileChromInfos) {
 
-                        var tracesPresent = false;
+                        let tracesPresent = false;
+                        let traces;
                         if (sampleFileChromInfos.rows && sampleFileChromInfos.rows.length > 0) {
-                            var rows = sampleFileChromInfos.rows;
-                            var uniqueTraces = [];
-                            var trace  = {};
+                            const rows = sampleFileChromInfos.rows;
+                            const uniqueTraces = [];
+                            const trace  = {};
 
-                            for (var i in rows) {
+                            for (let i in rows) {
                                 trace[rows[i]['TextId']] = rows[i];
                             }
 
-                            for (i in trace) {
+                            for (let i in trace) {
                                 uniqueTraces.push(trace[i]);
                             }
 
@@ -206,7 +226,7 @@
                             tracesPresent = true;
                         }
 
-                        var windowConfig = {
+                        const windowConfig = {
                             parent: this,
                             traces: tracesPresent ? traces : {} ,
                             tracesPresent: tracesPresent,
@@ -223,7 +243,7 @@
             },
 
             addNewMetric: function (metricType) {
-                var op = 'insert';
+                const op = 'insert';
                 if (metricType === 'custom') {
                     this.showCustomMetricWindow(op);
                 }
@@ -294,7 +314,7 @@
                     LABKEY.Query.saveRows({
                         commands: commands,
                         method: 'POST',
-                        success: function (data) {
+                        success: function () {
                             window.location = getReturnUrl();
                         },
                         failure: LABKEY.Utils.getCallbackWrapper(LABKEY.internal.ConfigureQCMetrics.onError, this, true)
diff --git a/resources/web/PanoramaPremium/window/AddNewMetricWindow.js b/resources/web/PanoramaPremium/window/AddNewMetricWindow.js
index 590553d2d..eba112162 100644
--- a/resources/web/PanoramaPremium/window/AddNewMetricWindow.js
+++ b/resources/web/PanoramaPremium/window/AddNewMetricWindow.js
@@ -37,7 +37,6 @@ Ext4.define('Panorama.Window.AddCustomMetricWindow', {
             schemaName: this.SCHEMA_NAME,
             success: function(queriesInfo) {
                 this.queries = queriesInfo.queries;
-                this.enabledqueries = queriesInfo.queries;
             }
         });
 
@@ -49,7 +48,6 @@ Ext4.define('Panorama.Window.AddCustomMetricWindow', {
             this.getQueriesCombo(),
             this.getMetricTypeCombo(),
             this.getYAxisLabelField(),
-            this.getEnabledQueriesCombo(),
             this.getQueryError(),
         ];
     },
@@ -150,28 +148,6 @@ Ext4.define('Panorama.Window.AddCustomMetricWindow', {
         return this.yAxisLabelField;
     },
 
-    getEnabledQueriesCombo: function() {
-        if(!this.enabledQueriesCombo) {
-            var config = Ext4.apply(this.getQueriesConfig('Enabled Query', 'enabledQueryName'), {
-                listeners: {
-                    scope: this,
-                    expand: function (field, options) {
-                        if (this.enabledqueries) {
-                            this.enabledQueriesCombo.bindStore(this.getQueriesStore());
-                        }
-                    }
-                }
-            });
-            this.enabledQueriesCombo = Ext4.create('Ext.form.field.ComboBox', config);
-
-            if(this.operation === this.update) {
-                this.enabledQueriesCombo.setValue(this.metric.EnabledQueryName);
-            }
-        }
-
-        return this.enabledQueriesCombo;
-    },
-
     getMetricTypeCombo: function() {
         if(!this.metricTypeCombo) {
             var metricTypeStore = Ext4.create('Ext.data.Store', {
@@ -320,8 +296,6 @@ Ext4.define('Panorama.Window.AddCustomMetricWindow', {
             newMetric.YAxisLabel = this.yAxisLabelField.getValue();
             newMetric.PrecursorScoped = this.metricTypeCombo.getValue();
 
-            newMetric.EnabledQueryName = this.enabledQueriesCombo.getValue();
-
             if(this.operation === this.update) {
                 newMetric.id = this.metric.id;
             }
diff --git a/src/org/labkey/targetedms/SkylineDocImporter.java b/src/org/labkey/targetedms/SkylineDocImporter.java
index 68f3ba578..5e6f30648 100644
--- a/src/org/labkey/targetedms/SkylineDocImporter.java
+++ b/src/org/labkey/targetedms/SkylineDocImporter.java
@@ -254,8 +254,7 @@ public TargetedMSRun importRun(RunInfo runInfo, PipelineJob job) throws IOExcept
 
             updateRunStatus(IMPORT_SUCCEEDED, STATUS_SUCCESS);
 
-            // We may have inserted the first set of data for a given metric
-            TargetedMSManager.get().clearCachedEnabledQCMetrics(run.getContainer());
+            TargetedMSManager.get().clearQCMetricCache(run.getContainer(), true);
 
             _progressMonitor.complete();
             return TargetedMSManager.getRun(_runId);
diff --git a/src/org/labkey/targetedms/TargetedMSController.java b/src/org/labkey/targetedms/TargetedMSController.java
index 11b76b13f..a376752e8 100644
--- a/src/org/labkey/targetedms/TargetedMSController.java
+++ b/src/org/labkey/targetedms/TargetedMSController.java
@@ -8159,6 +8159,17 @@ public long getId()
         }
     }
 
+    @RequiresPermission(AdminPermission.class)
+    public static class ClearQCMetricsCacheAction extends MutatingApiAction<Object>
+    {
+        @Override
+        public Object execute(Object form, BindException errors)
+        {
+            TargetedMSManager.get().clearQCMetricCache(getContainer(), true);
+            return new ApiSimpleResponse("success", true);
+        }
+    }
+
     public static class TargetedMSUrlsImpl implements TargetedMSUrls
     {
         public static TargetedMSUrlsImpl get()
diff --git a/src/org/labkey/targetedms/TargetedMSDataHandler.java b/src/org/labkey/targetedms/TargetedMSDataHandler.java
index 2a26138b6..5580b2942 100644
--- a/src/org/labkey/targetedms/TargetedMSDataHandler.java
+++ b/src/org/labkey/targetedms/TargetedMSDataHandler.java
@@ -290,7 +290,7 @@ public void runMoved(ExpData newData, Container container, Container targetConta
         }
 
         // Update the run
-        TargetedMSManager.moveRun(run, targetContainer, newRunLSID, newData.getRowId(), user);
+        TargetedMSManager.get().moveRun(run, targetContainer, newRunLSID, newData.getRowId(), user);
 
         // Delete the old entry in exp.data -- it is no longer linked to the run.
         ExpData oldData = ExperimentService.get().getExpData(oldDataRowID);
diff --git a/src/org/labkey/targetedms/TargetedMSManager.java b/src/org/labkey/targetedms/TargetedMSManager.java
index 131ae4d06..46ef668b3 100644
--- a/src/org/labkey/targetedms/TargetedMSManager.java
+++ b/src/org/labkey/targetedms/TargetedMSManager.java
@@ -162,7 +162,43 @@ private TargetedMSManager()
      * A cache to make it faster to render QC folders. A number of API calls come from the
      * client rendering the overview, all of which need to know the enabled configs.
      */
-    private static final Cache<Container, List<QCMetricConfiguration>> _metricCache = CacheManager.getCache(1000, TimeUnit.HOURS.toMillis(1), "Enabled QC metric configs");
+    private static final Cache<Container, List<QCMetricConfiguration>> _metricCache = CacheManager.getBlockingCache(1000, TimeUnit.HOURS.toMillis(1), "Enabled QC metric configs",
+            (c, argument) ->
+            {
+                try
+                {
+                    TargetedMSSchema schema = (TargetedMSSchema) argument;
+                    TableInfo metricsTable = schema.getTableOrThrow("qcMetricsConfig", null);
+                    List<QCMetricConfiguration> metrics = new TableSelector(metricsTable, null, new Sort(FieldKey.fromParts("Name"))).getArrayList(QCMetricConfiguration.class);
+
+                    OutlierGenerator.get().cachePrecursorMetricValues(schema, metrics);
+
+                    // Identify which precursor-scoped metrics have any cached data in this container
+                    SQLFragment sql = new SQLFragment("SELECT DISTINCT MetricId FROM (");
+                    sql.append(OutlierGenerator.get().getRawMetricSql(schema, metrics));
+                    sql.append(") y WHERE MetricValue IS NOT NULL");
+                    Set<Integer> cachedMetricIds = new HashSet<>(new SqlSelector(getSchema(), sql).getCollection(Integer.class));
+
+                    for (QCMetricConfiguration metric : metrics)
+                    {
+                        if (!cachedMetricIds.contains(metric.getId()))
+                        {
+                            metric.setStatus(QCMetricStatus.NoData);
+                        }
+                        else if (metric.getStatus() == null)
+                        {
+                            metric.setStatus(QCMetricStatus.DEFAULT);
+                        }
+                    }
+                    // Ensure we get a case-insensitive sort regardless of DB collation
+                    Collections.sort(metrics);
+                    return Collections.unmodifiableList(metrics);
+                }
+                catch (RuntimeException e)
+                {
+                    throw new PanoramaBadDataException("Failed to calculate metric values. Double-check the metric configurations and the backing queries. " + (e.getMessage() == null ? "" : e.getMessage()), e);
+                }
+            });
 
     public static TargetedMSManager get()
     {
@@ -551,6 +587,11 @@ public static TableInfo getTableQCTraceMetricValues()
         return getSchema().getTable(TargetedMSSchema.TABLE_QC_TRACE_METRIC_VALUES);
     }
 
+    public static TableInfo getTableInfoQCMetricCache()
+    {
+        return getSchema().getTable(TargetedMSSchema.TABLE_QC_METRIC_CACHE);
+    }
+
     public static TableInfo getTableInfoSkylineAuditLogEntry()
     {
         return getSchema().getTable(TargetedMSSchema.TABLE_SKYLINE_AUDITLOG_ENTRY);
@@ -1288,7 +1329,7 @@ public static void deleteRuns(List<Long> runIds, Container c, User user, boolean
         }
 
         // We may have deleted the last set of data for a given metric
-        containers.forEach(c2 -> TargetedMSManager.get().clearCachedEnabledQCMetrics(c2));
+        containers.forEach(c2 -> TargetedMSManager.get().clearQCMetricCache(c2, true));
 
         // Mark all the runs for deletion
         SQLFragment markDeleted = new SQLFragment("UPDATE " + getTableInfoRuns() + " SET ExperimentRunLSID = NULL, DataId = NULL, SkydDataId = NULL, Deleted=?, Modified=? ", Boolean.TRUE, new Date());
@@ -1602,7 +1643,7 @@ public static String getSampleFileUploadFile(long sampleFileId)
     /**
      * @return the file paths of the Skyline documents containing the given sample files
      */
-    @Nullable
+    @NotNull
     public static List<String> deleteSampleFilesAndDependencies(List<Long> sampleFileIds)
     {
         purgeDeletedSampleFiles(sampleFileIds);
@@ -1649,6 +1690,10 @@ public static void purgeDeletedSampleFiles(List<Long> sampleFileIds)
         // Delete from PrecursorAreaRatio (dependent of PrecursorChromInfo)
         execute(getTempChromInfoIdsDependentDeleteSql(getTableInfoPrecursorAreaRatio(), "PrecursorChromInfoId", precursorChromInfoIdsTempTableName));
 
+        // Delete from QCMetricCache (dependent of PrecursorChromInfo and SampleFile)
+        execute(getTempChromInfoIdsDependentDeleteSql(getTableInfoQCMetricCache(), "PrecursorChromInfoId", precursorChromInfoIdsTempTableName));
+        execute(new SQLFragment("DELETE FROM ").append(getTableInfoQCMetricCache()).append(whereClause));
+
         // Delete from PrecursorChromInfo
         execute(getTempChromInfoIdsDependentDeleteSql(getTableInfoPrecursorChromInfo(), "Id", precursorChromInfoIdsTempTableName));
 
@@ -2348,52 +2393,7 @@ private static Double getValue(Object o)
 
     public static List<QCMetricConfiguration> getAllQCMetricConfigurations(TargetedMSSchema schema)
     {
-        return _metricCache.get(schema.getContainer(), null, (c, argument) ->
-        {
-            TableInfo metricsTable = schema.getTableOrThrow("qcMetricsConfig", null);
-            SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("Status"), QCMetricStatus.Disabled.toString(), CompareType.NEQ_OR_NULL);
-            List<QCMetricConfiguration> metrics = new TableSelector(metricsTable, filter, new Sort(FieldKey.fromParts("Name"))).getArrayList(QCMetricConfiguration.class);
-
-            // We may encounter the same query to see if metrics have data more than once, so remember the values
-            // so we don't have to requery
-            Map<String, Boolean> hasDataQueries = new CaseInsensitiveHashMap<>();
-
-            for (QCMetricConfiguration metric : metrics)
-            {
-                if (metric.getStatus() == null)
-                {
-                    if (metric.getEnabledQueryName() == null)
-                    {
-                        metric.setStatus(QCMetricStatus.DEFAULT);
-                    }
-                    else
-                    {
-                        boolean hasData = hasDataQueries.computeIfAbsent(metric.getEnabledQueryName(), p ->
-                        {
-                            TableInfo enabledQuery = schema.getTable(metric.getEnabledQueryName(), null);
-                            if (enabledQuery != null)
-                            {
-                                return new TableSelector(enabledQuery).exists();
-                            }
-                            _log.warn("Could not find query " + schema.getName() + "." + metric.getEnabledQueryName() + " to determine if metric " + metric.getName() + " should be enabled in container " + c.getPath());
-                            return false;
-                        });
-
-                        if (!hasData)
-                        {
-                            metric.setStatus(QCMetricStatus.NoData);
-                        }
-                    }
-                }
-                if (metric.getStatus() == null)
-                {
-                    metric.setStatus(QCMetricStatus.DEFAULT);
-                }
-            }
-            // Ensure we get a case-insensitive sort regardless of DB collation
-            Collections.sort(metrics);
-            return Collections.unmodifiableList(metrics);
-        });
+        return _metricCache.get(schema.getContainer(), schema, null);
     }
     public static List<QCMetricConfiguration> getEnabledQCMetricConfigurations(TargetedMSSchema schema)
     {
@@ -2473,9 +2473,11 @@ select pci.id, COUNT(DISTINCT tci.Id) AS C FROM\s
         return maxCount != null ? maxCount.intValue() : 0;
     }
 
-    static void moveRun(TargetedMSRun run, Container newContainer, String newRunLSID, long newDataRowId, User user)
+    public void moveRun(TargetedMSRun run, Container newContainer, String newRunLSID, long newDataRowId, User user)
     {
         // MoveRunsTask.moveRun ensures a transaction
+        Container oldContainer = run.getContainer();
+
         SQLFragment updatePrecChromInfoSql = new SQLFragment("UPDATE ");
         updatePrecChromInfoSql.append(getTableInfoPrecursorChromInfo(), "");
         updatePrecChromInfoSql.append(" SET container = ?").add(newContainer);
@@ -2491,6 +2493,11 @@ static void moveRun(TargetedMSRun run, Container newContainer, String newRunLSID
         run.setDataId(newDataRowId);
         run.setContainer(newContainer);
         updateRun(run, user);
+
+        // Clear caches for both source and destination containers
+        if (oldContainer != null)
+            clearQCMetricCache(oldContainer, true);
+        clearQCMetricCache(newContainer, true);
     }
 
     private static void addParentRunsToChain(ArrayDeque<Long> chainRowIds, Map<Long, Long> replacedByMap, Long rowId)
@@ -2894,10 +2901,10 @@ else if (traceValue != null && values[i] >= traceValue)
 
     public static List<QCMetricConfiguration> getTraceMetricConfigurations(Container container, User user)
     {
-        return getEnabledQCMetricConfigurations(new TargetedMSSchema(user, container))
+        return getAllQCMetricConfigurations(new TargetedMSSchema(user, container))
                 .stream()
                 .filter(qcMetricConfiguration -> qcMetricConfiguration.getTraceName() != null)
-                .collect(Collectors.toList());
+                .toList();
     }
 
     public static List<IKeyword> getKeywords(long sequenceId)
@@ -2929,9 +2936,22 @@ public static Map<String,Object> getQCFolderDateRange(Container container)
         return new SqlSelector(getSchema(), sql).getMap();
     }
 
-    public void clearCachedEnabledQCMetrics(Container container)
+    /**
+     * Invalidate the stored QC metric value cache for this container.
+     * Called when underlying data or metric definitions change (e.g., Skyline import/delete, config edits).
+     */
+    public void clearQCMetricCache(Container container, boolean clearMetricValues)
     {
         getSchema().getScope().addCommitTask(() -> _metricCache.remove(container), DbScope.CommitTaskOption.IMMEDIATE, DbScope.CommitTaskOption.POSTCOMMIT, DbScope.CommitTaskOption.POSTROLLBACK);
+
+        if (clearMetricValues)
+        {
+            SQLFragment sql = new SQLFragment("DELETE FROM ");
+            sql.append(getTableInfoQCMetricCache());
+            sql.append(" WHERE Container = ?");
+            sql.add(container.getEntityId());
+            new SqlExecutor(getSchema()).execute(sql);
+        }
     }
 
     @NotNull
diff --git a/src/org/labkey/targetedms/TargetedMSModule.java b/src/org/labkey/targetedms/TargetedMSModule.java
index d6224e3cf..c0b7bd85d 100644
--- a/src/org/labkey/targetedms/TargetedMSModule.java
+++ b/src/org/labkey/targetedms/TargetedMSModule.java
@@ -183,10 +183,12 @@ public TargetedMSModule()
         SKYLINE_AUDIT_LEVEL_PROPERTY.setOptions(auditOptions);
         SKYLINE_AUDIT_LEVEL_PROPERTY.setDefaultValue("0");
         SKYLINE_AUDIT_LEVEL_PROPERTY.setCanSetPerContainer(true);
-        SKYLINE_AUDIT_LEVEL_PROPERTY.setDescription("Defines requirements for the integrity of the audit log uploaded together with a Skyline document. \n"+
-                "0 means that no audit log is required. If the log file is present in the uploaded file it will be parsed and loaded as is.\n " +
-                "1 means that audit log is required and its integrity will be verified using MD5 hash-based algorithm. If log integrity verification fails the document upload will be cancelled. \n" +
-                "2 means that audit log is required and its integrity will be verified using RSA-encryption algorithm. If log integrity verification fails the document upload will be cancelled.");
+        SKYLINE_AUDIT_LEVEL_PROPERTY.setDescription("""
+                Defines requirements for the integrity of the audit log uploaded together with a Skyline document.\s
+                0 means that no audit log is required. If the log file is present in the uploaded file it will be parsed and loaded as is.
+                 \
+                1 means that audit log is required and its integrity will be verified using MD5 hash-based algorithm. If log integrity verification fails the document upload will be cancelled.\s
+                2 means that audit log is required and its integrity will be verified using RSA-encryption algorithm. If log integrity verification fails the document upload will be cancelled.""");
         SKYLINE_AUDIT_LEVEL_PROPERTY.setShowDescriptionInline(true);
         addModuleProperty(SKYLINE_AUDIT_LEVEL_PROPERTY);
         //------------------------rr
@@ -229,7 +231,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 25.005;
+        return 25.006;
     }
 
     @Override
diff --git a/src/org/labkey/targetedms/TargetedMSSchema.java b/src/org/labkey/targetedms/TargetedMSSchema.java
index 8312d35ec..748540ab4 100644
--- a/src/org/labkey/targetedms/TargetedMSSchema.java
+++ b/src/org/labkey/targetedms/TargetedMSSchema.java
@@ -227,6 +227,7 @@ public class TargetedMSSchema extends UserSchema
     public static final String TABLE_QC_METRIC_EXCLUSION = "QCMetricExclusion";
     public static final String TABLE_QC_ENABLED_METRICS = "QCEnabledMetrics";
     public static final String TABLE_QC_TRACE_METRIC_VALUES = "QCTraceMetricValues";
+    public static final String TABLE_QC_METRIC_CACHE = "QCMetricCache";
 
     public static final String TABLE_GUIDE_SET = "GuideSet";
 
diff --git a/src/org/labkey/targetedms/model/RawMetricDataSet.java b/src/org/labkey/targetedms/model/RawMetricDataSet.java
index 3513e8edd..61a0727ad 100644
--- a/src/org/labkey/targetedms/model/RawMetricDataSet.java
+++ b/src/org/labkey/targetedms/model/RawMetricDataSet.java
@@ -181,7 +181,7 @@ public String getDataType()
         }
     }
 
-    @Nullable
+    @NotNull
     public String getSeriesLabel()
     {
         if (null != seriesLabel)
diff --git a/src/org/labkey/targetedms/outliers/OutlierGenerator.java b/src/org/labkey/targetedms/outliers/OutlierGenerator.java
index c0dfbe4fa..e133136ea 100644
--- a/src/org/labkey/targetedms/outliers/OutlierGenerator.java
+++ b/src/org/labkey/targetedms/outliers/OutlierGenerator.java
@@ -18,12 +18,13 @@
 import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
-import org.labkey.api.collections.IntHashMap;
+import org.labkey.api.action.SpringActionController;
 import org.labkey.api.collections.LongHashMap;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.RuntimeSQLException;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
+import org.labkey.api.data.SqlExecutor;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.query.QueryService;
@@ -72,7 +73,6 @@
 public class OutlierGenerator
 {
     private static final OutlierGenerator INSTANCE = new OutlierGenerator();
-    private static final DecimalFormat DECIMAL_FORMAT = new DecimalFormat("0.000");
 
     private OutlierGenerator() {}
 
@@ -81,7 +81,7 @@ public static OutlierGenerator get()
         return INSTANCE;
     }
 
-    private String getEachSeriesTypePlotDataSql(QCMetricConfiguration configuration, List<AnnotationGroup> annotationGroups)
+    private String getEachSeriesTypePlotDataSql(QCMetricConfiguration configuration)
     {
         String schemaName = "targetedms";
         String queryName = configuration.getQueryName();
@@ -93,7 +93,7 @@ private String getEachSeriesTypePlotDataSql(QCMetricConfiguration configuration,
         {
             sql.append("(SELECT 0 AS PrecursorChromInfoId, SampleFileId, ");
             sql.append(" metric.Name AS SeriesLabel, ");
-            sql.append("\nvalue as MetricValue, metric, ").append(configuration.getId()).append(" AS MetricId");
+            sql.append("\nvalue as MetricValue, Metric AS MetricId ");
             sql.append("\n FROM ").append(schemaName).append('.').append(TargetedMSManager.getTableQCTraceMetricValues().getName());
             sql.append(" WHERE metric = ").append(configuration.getId());
             sql.append(")");
@@ -102,51 +102,15 @@ private String getEachSeriesTypePlotDataSql(QCMetricConfiguration configuration,
         {
             sql.append("(SELECT PrecursorChromInfoId, SampleFileId, ");
             sql.append(" CAST(IFDEFINED(SeriesLabel) AS VARCHAR) AS SeriesLabel, ");
-            sql.append("\nMetricValue, 0 as metric, ").append(configuration.getId()).append(" AS MetricId");
-
+            sql.append("\nMetricValue, ").append(configuration.getId()).append(" AS MetricId");
             sql.append("\n FROM ").append(schemaName).append('.').append(queryName);
-
-            if (!annotationGroups.isEmpty())
-            {
-                sql.append(" WHERE ");
-                StringBuilder filterClause = new StringBuilder("SampleFileId.ReplicateId IN (");
-                var intersect = "";
-                var selectSql = "(SELECT ReplicateId FROM targetedms.ReplicateAnnotation WHERE ";
-                for (AnnotationGroup annotation : annotationGroups)
-                {
-                    filterClause.append(intersect)
-                            .append(selectSql)
-                            .append(" Name='")
-                            .append(annotation.getName().replace("'", "''"))
-                            .append("'");
-
-
-                    var annotationValues = annotation.getValues();
-                    if (!annotationValues.isEmpty())
-                    {
-                        var quoteEscapedVals = annotationValues.stream().map(s -> s.replace("'", "''")).toList( );
-                        var vals = "'" + StringUtils.join(quoteEscapedVals, "','") + "'";
-                        filterClause.append(" AND  Value IN (").append(vals).append(" )");
-                    }
-                    filterClause.append(" ) ");
-                    intersect = " INTERSECT ";
-                }
-                filterClause.append(") ");
-                sql.append(filterClause);
-            }
-            if (configuration.getTraceName() != null)
-            {
-                sql.append(" WHERE metric = ").append(configuration.getId());
-            }
             sql.append(")");
         }
         return sql.toString();
     }
 
     /** @return LabKey SQL to fetch all the values for the specified metrics */
-    private String queryContainerSampleFileRawData(List<QCMetricConfiguration> configurations, Date startDate,
-                                                   Date endDate, List<AnnotationGroup> annotationGroups,
-                                                   boolean showExcluded)
+    private String queryContainerSampleFileRawData(List<QCMetricConfiguration> configurations)
     {
         // Copy so that we can use our preferred sort
         configurations = new ArrayList<>(configurations);
@@ -166,44 +130,42 @@ private String queryContainerSampleFileRawData(List<QCMetricConfiguration> confi
         {
             if (alreadyAdded.add(Pair.of(configuration.getId(), 1)))
             {
-                sql.append(sep).append(getEachSeriesTypePlotDataSql(configuration, annotationGroups));
+                sql.append(sep).append(getEachSeriesTypePlotDataSql(configuration));
             }
             sep = "\nUNION ALL\n";
         }
-
         sql.append(") X");
-        sql.append("\nINNER JOIN SampleFile sf ON X.SampleFileId = sf.Id");
-        if (null != startDate || null != endDate)
+        return sql.toString();
+    }
+
+    /**
+     * We cache all precursor-scoped metrics in targetedms.QCMetricCache for performance.
+     * Run-scoped metrics are not cached like this as they are fast enough to query directly from the backing tables
+     * like targetedms.SampleFile and targetedms.QCTraceMetricValues.
+     */
+    public void cachePrecursorMetricValues(TargetedMSSchema schema, List<QCMetricConfiguration> allMetrics)
+    {
+        SQLFragment existingSql = new SQLFragment("SELECT Container FROM ").append(TargetedMSManager.getTableInfoQCMetricCache(), "c").append(" WHERE Container = ?").add(schema.getContainer());
+        if (!new SqlSelector(schema.getDbSchema(), existingSql).exists())
         {
-            var sqlSeparator = "WHERE";
+            List<QCMetricConfiguration> precursorMetrics = allMetrics.stream()
+                    .filter(QCMetricConfiguration::isPrecursorScoped)
+                    .toList();
 
-            if (null != startDate)
-            {
-                sql.append("\n").append(sqlSeparator);
-                sql.append(" sf.AcquiredTime >= '");
-                sql.append(startDate);
-                sql.append("' ");
-                sqlSeparator = "AND";
-            }
+            String computeAllSql = queryContainerSampleFileRawData(precursorMetrics);
+            TableInfo tiAll = QueryService.get().createTable(schema, computeAllSql, null, true);
 
-            if (null != endDate)
+            try (var ignored = SpringActionController.ignoreSqlUpdates())
             {
-                sql.append("\n").append(sqlSeparator);
-                sql.append("\n sf.AcquiredTime < TIMESTAMPADD('SQL_TSI_DAY', 1, CAST('");
-                sql.append(endDate);
-                sql.append("' AS TIMESTAMP))");
+                SQLFragment insertAll = new SQLFragment();
+                insertAll.append("INSERT INTO ");
+                insertAll.append(TargetedMSManager.getTableInfoQCMetricCache()).append(" (Container, MetricId, PrecursorChromInfoId, SampleFileId, MetricValue, SeriesLabel) ");
+                insertAll.append(" SELECT ?, lk.MetricId, lk.PrecursorChromInfoId, lk.SampleFileId, lk.MetricValue, lk.SeriesLabel FROM ");
+                insertAll.append(tiAll, "lk");
+                insertAll.add(schema.getContainer());
+                new SqlExecutor(TargetedMSManager.getSchema()).execute(insertAll);
             }
         }
-        else
-        {
-            sql.append("\nWHERE sf.AcquiredTime IS NOT NULL");
-        }
-        if (!showExcluded)
-        {
-            sql.append(" AND sf.Excluded = false");
-        }
-
-        return sql.toString();
     }
 
     public List<RawMetricDataSet> getRawMetricDataSets(TargetedMSSchema schema, List<QCMetricConfiguration> configurations, Date startDate, Date endDate, List<AnnotationGroup> annotationGroups, boolean showExcluded, boolean showExcludedPrecursors)
@@ -219,55 +181,110 @@ public List<RawMetricDataSet> getRawMetricDataSets(TargetedMSSchema schema, List
             sampleFiles.put(sf.getId(), sf);
         }
 
-        String labkeySQL = queryContainerSampleFileRawData(configurations, startDate, endDate, annotationGroups, showExcluded);
-
-        // Use strictColumnList = false to avoid a potentially expensive injected join for the Container via lookups
-        TableInfo ti = QueryService.get().createTable(schema, labkeySQL, null, true);
+        // Load precursor info and metric map
+        Map<Long, Object> excludedPrecursorIds = new LongHashMap<>();
+        Map<Long, RawMetricDataSet.PrecursorInfo> precursors;
+        try
+        {
+            precursors = loadPrecursors(schema, excludedPrecursorIds, showExcludedPrecursors);
+        }
+        catch (SQLException e)
+        {
+            throw new RuntimeSQLException(e);
+        }
+        Map<Integer, QCMetricConfiguration> metrics = new HashMap<>();
+        configurations.forEach(m -> metrics.put(m.getId(), m));
 
-        SQLFragment sql = new SQLFragment("SELECT lk.*, pci.PrecursorId ");
-        sql.append(" FROM ");
-        sql.append(ti, "lk");
+        SQLFragment sql = new SQLFragment("SELECT x.*, pci.PrecursorId FROM (");
+        sql.append(getRawMetricSql(schema, configurations));
+        sql.append(") x ");
         sql.append(" LEFT OUTER JOIN ");
         sql.append(TargetedMSManager.getTableInfoPrecursorChromInfo(), "pci");
-        sql.append(" ON lk.PrecursorChromInfoId = pci.Id ");
+        sql.append(" ON x.PrecursorChromInfoId = pci.Id ");
+        sql.append(" INNER JOIN ");
+        sql.append(TargetedMSManager.getTableInfoSampleFile(), "sf");
+        sql.append(" ON x.SampleFileId = sf.Id ");
 
-        try
+        if (null != startDate || null != endDate)
         {
-            Map<Long, Object> excludedPrecursorIds = new LongHashMap<>();
-            Map<Long, RawMetricDataSet.PrecursorInfo> precursors = loadPrecursors(schema, excludedPrecursorIds, showExcludedPrecursors);
-
-            Map<Integer, QCMetricConfiguration> metrics = new IntHashMap<>();
-            configurations.forEach(m -> metrics.put(m.getId(), m));
-
-            try (ResultSet rs = new SqlSelector(TargetedMSManager.getSchema(), sql).getResultSet(false))
+            if (null != startDate)
             {
-                while (rs.next())
-                {
-                    long sampleFileId = rs.getLong("SampleFileId");
-                    Long precursorId = getLong(rs, "PrecursorId");
+                sql.append(" AND sf.AcquiredTime >= ?");
+                sql.add(startDate);
+            }
+            if (null != endDate)
+            {
+                sql.append(" AND sf.AcquiredTime < ?");
+                // Add one day to be exclusive upper bound, mimicking TIMESTAMPADD('SQL_TSI_DAY', 1, endDate)
+                sql.add(new Date(endDate.getTime() + 24L * 60L * 60L * 1000L));
+            }
+        }
+        else
+        {
+            sql.append(" AND sf.AcquiredTime IS NOT NULL");
+        }
+        if (!showExcluded)
+        {
+            sql.append(" AND sf.ReplicateId NOT IN (SELECT ReplicateId FROM ");
+            sql.append(TargetedMSManager.getTableInfoQCMetricExclusion(), "x");
+            sql.append(" WHERE x.MetricId IS NULL)");
+        }
 
-                    if (excludedPrecursorIds.containsKey(precursorId))
-                        continue;
+        if (!annotationGroups.isEmpty())
+        {
+            sql.append(" AND sf.ReplicateId IN (");
+            String intersect = "";
+            for (AnnotationGroup annotation : annotationGroups)
+            {
+                sql.append(intersect).append(" SELECT ReplicateId FROM ")
+                    .append(TargetedMSManager.getTableInfoReplicateAnnotation(), "ra").append(" WHERE ra.Name = ?");
+                sql.add(annotation.getName());
 
-                    // Sample-scoped metrics won't have an associated precursor
-                    RawMetricDataSet.PrecursorInfo precursor = null;
-                    if (precursorId != null)
+                List<String> vals = annotation.getValues();
+                if (!vals.isEmpty())
+                {
+                    sql.append(" AND ra.Value IN (");
+                    String vsep = "";
+                    for (String v : vals)
                     {
-                        precursor = precursors.get(precursorId);
-                        if (precursor == null)
-                        {
-                            throw new IllegalStateException("Could not find Precursor with Id " + precursorId);
-                        }
+                        sql.append(vsep).append("?");
+                        sql.add(v);
+                        vsep = ",";
                     }
+                    sql.append(")");
+                }
+                intersect = " INTERSECT ";
+            }
+            sql.append(")");
+        }
+
+        try (ResultSet rs = new SqlSelector(TargetedMSManager.getSchema(), sql).getResultSet(false))
+        {
+            while (rs.next())
+            {
+                int metricId = rs.getInt("MetricId");
+                long sampleFileId = rs.getLong("SampleFileId");
+                Long precursorId = getLong(rs, "PrecursorId");
 
-                    RawMetricDataSet row = new RawMetricDataSet(sampleFiles.get(sampleFileId), precursor);
+                if (excludedPrecursorIds.containsKey(precursorId))
+                    continue;
 
-                    row.setMetric(metrics.get(rs.getInt("MetricId"))); // this datarow is not setting the correct metric
-                    row.setSeriesLabel(rs.getString("SeriesLabel"));
-                    row.setPrecursorChromInfoId(getLong(rs, "PrecursorChromInfoId"));
-                    row.setMetricValue(getDouble(rs, "MetricValue"));
-                    result.add(row);
+                RawMetricDataSet.PrecursorInfo precursor = null;
+                if (precursorId != null)
+                {
+                    precursor = precursors.get(precursorId);
+                    if (precursor == null)
+                    {
+                        throw new IllegalStateException("Could not find Precursor with Id " + precursorId);
+                    }
                 }
+
+                RawMetricDataSet row = new RawMetricDataSet(sampleFiles.get(sampleFileId), precursor);
+                row.setMetric(metrics.get(metricId));
+                row.setSeriesLabel(rs.getString("SeriesLabel"));
+                row.setPrecursorChromInfoId(getLong(rs, "PrecursorChromInfoId"));
+                row.setMetricValue(getDouble(rs, "MetricValue"));
+                result.add(row);
             }
         }
         catch (SQLException e)
@@ -281,6 +298,46 @@ public List<RawMetricDataSet> getRawMetricDataSets(TargetedMSSchema schema, List
         return result;
     }
 
+    public SQLFragment getRawMetricSql(TargetedMSSchema schema, List<QCMetricConfiguration> configurations)
+    {
+        // Split configurations into cacheable (precursor-scoped) vs direct-query (run-scoped)
+        List<QCMetricConfiguration> runScoped = configurations.stream()
+                .filter(c -> !c.isPrecursorScoped())
+                .toList();
+        List<QCMetricConfiguration> precursorScoped = configurations.stream()
+                .filter(QCMetricConfiguration::isPrecursorScoped)
+                .toList();
+
+        // Read requested precursor values from the cache with all the filters
+        SQLFragment sql = new SQLFragment();
+
+        String separator = "";
+        if (!precursorScoped.isEmpty())
+        {
+            sql.append("SELECT c.PrecursorChromInfoId, c.SampleFileId, c.SeriesLabel, c.MetricValue, c.MetricId ");
+            sql.append(" FROM ");
+            sql.append(TargetedMSManager.getTableInfoQCMetricCache(), "c");
+            sql.append(" WHERE c.Container = ?\n");
+            sql.add(schema.getContainer());
+            sql.append(" AND c.MetricId IN (");
+            sql.append(StringUtils.repeat("?", ",", precursorScoped.size()));
+            sql.addAll(precursorScoped.stream().map(QCMetricConfiguration::getId).toList());
+            sql.append(")");
+            separator = "\nUNION ALL\n";
+        }
+
+        if (!runScoped.isEmpty())
+        {
+            sql.append(separator);
+            String runScopedLabKeySql = queryContainerSampleFileRawData(runScoped);
+            TableInfo ti = QueryService.get().createTable(schema, runScopedLabKeySql, null, true);
+            sql.append("SELECT lk.* ");
+            sql.append(" FROM ");
+            sql.append(ti, "lk");
+        }
+        return sql;
+    }
+
     /**
      * Fetch all the precursors in this folder. Loaded separately from the metric values because a given precursor will
      * have many metrics, so for DB query and Java memory use it's more efficient to not flatten them into a single
diff --git a/src/org/labkey/targetedms/pipeline/TargetedMSImportTask.java b/src/org/labkey/targetedms/pipeline/TargetedMSImportTask.java
index 50ebc69e7..20a07cff8 100644
--- a/src/org/labkey/targetedms/pipeline/TargetedMSImportTask.java
+++ b/src/org/labkey/targetedms/pipeline/TargetedMSImportTask.java
@@ -83,7 +83,7 @@ public Factory()
         }
 
         @Override
-        public PipelineJob.Task createTask(PipelineJob job)
+        public TargetedMSImportTask createTask(PipelineJob job)
         {
             return new TargetedMSImportTask(this, job);
         }
diff --git a/src/org/labkey/targetedms/query/QCEnabledMetricsTable.java b/src/org/labkey/targetedms/query/QCEnabledMetricsTable.java
index f3bdddfdd..f87565135 100644
--- a/src/org/labkey/targetedms/query/QCEnabledMetricsTable.java
+++ b/src/org/labkey/targetedms/query/QCEnabledMetricsTable.java
@@ -77,7 +77,7 @@ public QueryUpdateService getUpdateService()
             @Override
             protected Map<String, Object> _insert(User user, Container c, Map<String, Object> row) throws SQLException, ValidationException
             {
-                TargetedMSManager.get().clearCachedEnabledQCMetrics(c);
+                TargetedMSManager.get().clearQCMetricCache(c, false);
                 validateBounds(row);
                 return super._insert(user, c, row);
             }
@@ -125,7 +125,7 @@ private static void validateBounds(Map<String, Object> row) throws ValidationExc
             @Override
             protected Map<String, Object> _update(User user, Container c, Map<String, Object> row, Map<String, Object> oldRow, Object[] keys) throws SQLException, ValidationException
             {
-                TargetedMSManager.get().clearCachedEnabledQCMetrics(c);
+                TargetedMSManager.get().clearQCMetricCache(c, false);
                 validateBounds(row);
                 return super._update(user, c, row, oldRow, keys);
             }
@@ -133,7 +133,7 @@ protected Map<String, Object> _update(User user, Container c, Map<String, Object
             @Override
             protected void _delete(Container c, Map<String, Object> row) throws InvalidKeyException
             {
-                TargetedMSManager.get().clearCachedEnabledQCMetrics(c);
+                TargetedMSManager.get().clearQCMetricCache(c, false);
                 super._delete(c, row);
             }
         };
diff --git a/src/org/labkey/targetedms/query/QCMetricConfigurationTable.java b/src/org/labkey/targetedms/query/QCMetricConfigurationTable.java
index 78cd35ae4..1dfaca3dd 100644
--- a/src/org/labkey/targetedms/query/QCMetricConfigurationTable.java
+++ b/src/org/labkey/targetedms/query/QCMetricConfigurationTable.java
@@ -36,6 +36,7 @@
 import org.labkey.api.security.permissions.AdminPermission;
 import org.labkey.api.security.permissions.Permission;
 import org.labkey.api.security.permissions.ReadPermission;
+import org.labkey.api.util.StringExpressionFactory;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSRun;
 import org.labkey.targetedms.TargetedMSSchema;
@@ -44,7 +45,6 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
-import java.util.stream.Collectors;
 
 import static org.labkey.api.exp.api.ExperimentService.asInteger;
 
@@ -56,9 +56,8 @@ public QCMetricConfigurationTable(TargetedMSSchema schema, ContainerFilter cf)
         wrapAllColumns(true);
         TargetedMSTable.fixupLookups(this);
         setInsertURL(LINK_DISABLER);
-        setDeleteURL(LINK_DISABLER);
-        setUpdateURL(LINK_DISABLER);
         setImportURL(LINK_DISABLER);
+        getMutableColumnOrThrow("QueryName").setURL(StringExpressionFactory.createURL("/query-executeQuery.view?schemaName=targetedms&queryName=${QueryName}"));
     }
 
     @Override
@@ -106,7 +105,6 @@ protected QCMetricConfigurationTableUpdateService(QCMetricConfigurationTable que
         protected Map<String, Object> insertRow(User user, Container container, Map<String, Object> row) throws DuplicateKeyException, ValidationException, QueryUpdateServiceException, SQLException
         {
             var insertedRow = super.insertRow(user, container, row);
-            TargetedMSManager.get().clearCachedEnabledQCMetrics(container);
             calculateAndInsertTraceValuesForMetric(asInteger(insertedRow.get("Id")), container, user);
             return insertedRow;
         }
@@ -117,7 +115,6 @@ protected Map<String, Object> updateRow(User user, Container container, Map<Stri
             var updatedRow = super.updateRow(user, container, row, oldRow, configParameters);
             int metricId = asInteger(updatedRow.get("Id"));
             deleteTraceValueForMetric(metricId, container);
-            TargetedMSManager.get().clearCachedEnabledQCMetrics(container);
             calculateAndInsertTraceValuesForMetric(metricId, container, user);
             return updatedRow;
         }
@@ -125,8 +122,8 @@ protected Map<String, Object> updateRow(User user, Container container, Map<Stri
         @Override
         protected Map<String, Object> deleteRow(User user, Container container, Map<String, Object> oldRow) throws InvalidKeyException, QueryUpdateServiceException, SQLException
         {
-            TargetedMSManager.get().clearCachedEnabledQCMetrics(container);
             deleteTraceValueForMetric(asInteger(oldRow.get("id")), container);
+            TargetedMSManager.get().clearQCMetricCache(container, true);
             return super.deleteRow(user, container, oldRow);
         }
 
@@ -144,11 +141,20 @@ private void deleteTraceValueForMetric(int metricId, Container container)
 
         private void calculateAndInsertTraceValuesForMetric(int metricId, Container container, User user)
         {
+            // Make sure that we pick up the new metric
+            TargetedMSManager.get().clearQCMetricCache(container, true);
+
             var qcMetricConfigurations = TargetedMSManager
-                .getEnabledQCMetricConfigurations(_queryTable.getUserSchema())
+                .getAllQCMetricConfigurations(_queryTable.getUserSchema())
                 .stream()
                 .filter(qcMetricConfiguration -> qcMetricConfiguration.getId() == metricId)
-                .collect(Collectors.toList());
+                .toList();
+
+            if (qcMetricConfigurations.isEmpty())
+            {
+                throw new IllegalStateException("No QCMetricConfiguration found for Id " + metricId);
+            }
+
             var runsInContainer = TargetedMSManager.getRunsInContainer(container);
 
             for (TargetedMSRun run : runsInContainer)
@@ -156,6 +162,9 @@ private void calculateAndInsertTraceValuesForMetric(int metricId, Container cont
                 var qcTraceMetricValues = TargetedMSManager.calculateTraceMetricValues(qcMetricConfigurations, run);
                 qcTraceMetricValues.forEach(qcTraceMetricValue -> Table.insert(user, TargetedMSManager.getTableQCTraceMetricValues(), qcTraceMetricValue));
             }
+
+            // Clear again so that we have the right state for the presence/absence of data
+            TargetedMSManager.get().clearQCMetricCache(container, false);
         }
     }
 }
diff --git a/test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java b/test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java
index 46e92e305..4f8328dac 100644
--- a/test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java
+++ b/test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java
@@ -23,6 +23,7 @@
 import org.labkey.test.components.ext4.ComboBox;
 import org.labkey.test.components.ext4.RadioButton;
 import org.labkey.test.components.ext4.Window;
+import org.labkey.test.pages.panoramapremium.ConfigureMetricsUIPage;
 import org.labkey.test.util.Ext4Helper;
 import org.labkey.test.util.LogMethod;
 import org.labkey.test.util.LoggedParam;
@@ -740,6 +741,13 @@ public Locator.XPathLocator getBubbleContent()
         return hopscotchBubble.append(Locator.byClass("hopscotch-bubble-content").append(Locator.byClass("hopscotch-content").withText()));
     }
 
+    public ConfigureMetricsUIPage clickConfigureQCMetrics()
+    {
+        clickMenuItem("Configure QC Metrics");
+        getWrapper().waitForElement(Locator.tagWithText("button", ConfigureMetricsUIPage.ADD_NEW_CUSTOM_METRIC));
+        return new ConfigureMetricsUIPage(getDriver());
+    }
+
     public enum Scale
     {
         LINEAR("Linear"),
diff --git a/test/src/org/labkey/test/components/targetedms/QCSummaryWebPart.java b/test/src/org/labkey/test/components/targetedms/QCSummaryWebPart.java
index e08480a03..ac95bbc8c 100644
--- a/test/src/org/labkey/test/components/targetedms/QCSummaryWebPart.java
+++ b/test/src/org/labkey/test/components/targetedms/QCSummaryWebPart.java
@@ -19,6 +19,7 @@
 import org.labkey.test.WebDriverWrapper;
 import org.labkey.test.components.BodyWebPart;
 import org.labkey.test.components.Component;
+import org.labkey.test.pages.panoramapremium.ConfigureMetricsUIPage;
 import org.openqa.selenium.WebDriver;
 import org.openqa.selenium.WebElement;
 
@@ -99,7 +100,15 @@ protected Elements newElementCache()
         return new Elements();
     }
 
-    public class Elements extends BodyWebPart.ElementCache
+    public ConfigureMetricsUIPage clickConfigureQCMetrics()
+    {
+        clickMenuItem("Configure QC Metrics");
+        getWrapper().waitForElement(Locator.tagWithText("button", ConfigureMetricsUIPage.ADD_NEW_CUSTOM_METRIC));
+        return new ConfigureMetricsUIPage(getDriver());
+
+    }
+
+    public class Elements extends BodyWebPart<?>.ElementCache
     {
         private List<QcSummaryTile> summaryTiles;
         public List<QcSummaryTile> summaryTiles()
diff --git a/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java b/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java
index abb1555c0..bc5050327 100644
--- a/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java
+++ b/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java
@@ -9,14 +9,18 @@
 import org.labkey.test.pages.PortalBodyPanel;
 import org.labkey.test.util.Ext4Helper;
 import org.openqa.selenium.NoSuchElementException;
+import org.openqa.selenium.WebDriver;
 
 import java.util.Map;
 
 public class ConfigureMetricsUIPage extends PortalBodyPanel
 {
-    public ConfigureMetricsUIPage(BaseWebDriverTest test)
+
+    public static final String ADD_NEW_CUSTOM_METRIC = "Add New Custom Metric";
+
+    public ConfigureMetricsUIPage(WebDriver driver)
     {
-        super(test.getDriver());
+        super(driver);
     }
 
     public ConfigureMetricsUIPage setLeveyJennings(String metric, @Nullable String lowerBound, @Nullable String upperBound)
@@ -111,7 +115,7 @@ public String clickSaveExpectingError()
 
     public void addNewCustomMetric(Map<CustomMetricProperties, String> metricProperties)
     {
-        click(Locator.tagWithText("button", "Add New Custom Metric"));
+        click(Locator.tagWithText("button", ADD_NEW_CUSTOM_METRIC));
         waitForElement(Ext4Helper.Locators.window("Add New Metric"));
         Window<?> metricWindow = new Window.WindowFinder(getDriver()).withTitle("Add New Metric").waitFor();
         editCustomMetricValues(metricWindow, metricProperties);
@@ -190,6 +194,12 @@ else if (prop.formLabel != null)
         waitForElement(Locator.linkWithText(metricProperties.get(ConfigureMetricsUIPage.TraceMetricProperties.metricName)));
     }
 
+    public void clearMetricCache()
+    {
+        clickButton("Clear Cached Metric Values", 0);
+        waitForText("Cleared cached metrics");
+    }
+
     public enum MetricType
     {
         Precursor,
@@ -201,8 +211,7 @@ public enum CustomMetricProperties
         metricName("Name", false),
         queryName("Metrics Query", true),
         yAxisLabel("Y-Axis Label", false),
-        metricType("Metric Type", true),
-        enabledQueryName("Enabled Query", true);
+        metricType("Metric Type", true);
 
         private final String formLabel;
         private final boolean isSelect;
diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java
index 5f9208cf4..6dfbdff7d 100644
--- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java
+++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java
@@ -63,13 +63,7 @@ public void testIsotopologueMetric()
         assertTextPresent("ELA\u2026GFk", "ELA\u2026PV\u2026", "ELA\u2026Pv\u2026", "ELA\u2026p\u2026");
 
         log("Verifying isotopologue is present while configuring the metric");
-        qcPlotsWebPart.clickMenuItem("Configure QC Metrics");
+        qcPlotsWebPart.clickConfigureQCMetrics();
         waitForText("Isotopologue Accuracy", "Isotopologue LOD", "Isotopologue LOQ", "Isotopologue Regression RSquared");
-
-        log("Verifying that two new metric properties are added");
-        clickButton("Add New Custom Metric", 0);
-        Window<?> metricWindow = new Window.WindowFinder(getDriver()).withTitle("Add New Metric").waitFor();
-        assertElementPresent(Locator.name(ConfigureMetricsUIPage.CustomMetricProperties.enabledQueryName.name()));
-
     }
 }
diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSPremiumTest.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSPremiumTest.java
index 12b27823f..4b28cd95f 100644
--- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSPremiumTest.java
+++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSPremiumTest.java
@@ -1,6 +1,5 @@
 package org.labkey.test.tests.panoramapremium;
 
-import org.labkey.test.Locator;
 import org.labkey.test.components.targetedms.QCPlotsWebPart;
 import org.labkey.test.pages.panoramapremium.ConfigureMetricsUIPage;
 import org.labkey.test.pages.targetedms.PanoramaDashboard;
@@ -16,9 +15,7 @@ public ConfigureMetricsUIPage goToConfigureMetricsUI()
     {
         PanoramaDashboard qcDashboard = goToDashboard();
         QCPlotsWebPart qcPlotsWebPart = qcDashboard.getQcPlotsWebPart();
-        qcPlotsWebPart.clickMenuItem("Configure QC Metrics");
-        waitForElement(Locator.tagWithText("button", "Add New Custom Metric"));
-        return new ConfigureMetricsUIPage(this);
+        return qcPlotsWebPart.clickConfigureQCMetrics();
     }
 
     protected void verifyMetricNotPresent(QCPlotsWebPart qcPlotsWebPart, String metricName)
diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java
index b059b7c15..595bc8864 100644
--- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java
+++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java
@@ -179,6 +179,20 @@ public void testAddNewMetric()
 
         log("Verifying new metric got edited");
         waitForElement(Locator.linkWithText(metricName2));
+        configureUI.setLeveyJennings(metricName2, "-3", "3");
+        configureUI.clickSave();
+        qcPlotsWebPart = qcDashboard.getQcPlotsWebPart();
+        List<String> metricOptions = getMetric1TypeOptions(qcPlotsWebPart);
+        assertTrue("Didn't find '" + metricName2 + "' in :" + metricOptions, metricOptions.contains(metricName2));
+        goToConfigureMetricsUI().deleteMetric(metricName2);
+        goToDashboard();
+        metricOptions = getMetric1TypeOptions(qcPlotsWebPart);
+        assertFalse("Found '" + metricName2 + "' in :" + metricOptions, metricOptions.contains(metricName2));
+    }
+
+    private static List<String> getMetric1TypeOptions(QCPlotsWebPart qcPlotsWebPart)
+    {
+        return qcPlotsWebPart.getMetric1TypeOptions();
     }
 
     @Test
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java
index e6d67c340..64c3c0a9c 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java
@@ -58,8 +58,7 @@ public void testHeatMapColorAndValues()
         log("Updating the Metric type values");
         goToProjectHome();
         QCPlotsWebPart qcPlotsWebPart = new PanoramaDashboard(this).getQcPlotsWebPart();
-        qcPlotsWebPart.clickMenuItem("Configure QC Metrics");
-        ConfigureMetricsUIPage configureQCMetrics = new ConfigureMetricsUIPage(this);
+        ConfigureMetricsUIPage configureQCMetrics = qcPlotsWebPart.clickConfigureQCMetrics();
         configureQCMetrics.setFixedDeviationFromMean(QCPlotsWebPart.MetricType.PRECURSOR_AREA, "-5", "5")
                 .clickSave();
 
@@ -149,8 +148,7 @@ public void testMetricUsagePeptideSummaryHeatmap()
         log("Updating the Metric type values");
         goToProjectHome();
         QCPlotsWebPart qcPlotsWebPart = new PanoramaDashboard(this).getQcPlotsWebPart();
-        qcPlotsWebPart.clickMenuItem("Configure QC Metrics");
-        ConfigureMetricsUIPage configureQCMetrics = new ConfigureMetricsUIPage(this);
+        ConfigureMetricsUIPage configureQCMetrics = qcPlotsWebPart.clickConfigureQCMetrics();
         configureQCMetrics.setShowMetricNoOutlier(QCPlotsWebPart.MetricType.TRANSITION_MASS_ERROR)
                 .setFixedValueCutOff(QCPlotsWebPart.MetricType.RETENTION, "-15", "15")
                 .disableMetric(QCPlotsWebPart.MetricType.TOTAL_PEAK.toString())
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
index ef1afc83f..7d2cd9077 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
@@ -11,10 +11,13 @@
 import org.labkey.test.pages.panoramapremium.ConfigureMetricsUIPage;
 import org.labkey.test.pages.targetedms.PanoramaDashboard;
 import org.labkey.test.tests.panoramapremium.TargetedMSPremiumTest;
+import org.labkey.test.util.DataRegion;
+import org.labkey.test.util.DataRegionTable;
 import org.openqa.selenium.WebElement;
 
 import java.util.Arrays;
 import java.util.List;
+import java.util.Map;
 import java.util.regex.Pattern;
 
 @Category({})
@@ -53,11 +56,10 @@ public void testInconsistentMetricDisplay()
         setupSubfolder(getProjectName(), SUBFOLDER_1, FolderType.QC);
         importData(SProCoP_FILE);
         navigateToFolder(getProjectName(), SUBFOLDER_1);
-        new PanoramaDashboard(this).getQcSummaryWebPart().clickMenuItem("Configure QC Metrics");
-        ConfigureMetricsUIPage configureQCMetrics = new ConfigureMetricsUIPage(this);
-        configureQCMetrics.disableMetric("Precursor Area")
-                .disableMetric("Retention Time")
-                .disableMetric("Transition Area")
+        ConfigureMetricsUIPage configureQCMetrics = new PanoramaDashboard(this).getQcSummaryWebPart().clickConfigureQCMetrics();
+        configureQCMetrics.disableMetric(QCPlotsWebPart.MetricType.PRECURSOR_AREA.toString())
+                .disableMetric(QCPlotsWebPart.MetricType.RETENTION.toString())
+                .disableMetric(QCPlotsWebPart.MetricType.TRANSITION_AREA.toString())
                 .clickSave();
 
         log("Create subfolder, import data and configure custom metrics in " + SUBFOLDER_2);
@@ -65,9 +67,8 @@ public void testInconsistentMetricDisplay()
         setupSubfolder(getProjectName(), SUBFOLDER_2, FolderType.QC);
         importData(SProCoP_FILE);
         navigateToFolder(getProjectName(), SUBFOLDER_2);
-        new PanoramaDashboard(this).getQcSummaryWebPart().clickMenuItem("Configure QC Metrics");
-        configureQCMetrics = new ConfigureMetricsUIPage(this);
-        configureQCMetrics.disableMetric("Precursor Area")
+        configureQCMetrics = new PanoramaDashboard(this).getQcSummaryWebPart().clickConfigureQCMetrics();
+        configureQCMetrics.disableMetric(QCPlotsWebPart.MetricType.PRECURSOR_AREA.toString())
                 .clickSave();
 
         log("Verify the data is displayed correctly on parent folder");
@@ -78,13 +79,43 @@ public void testInconsistentMetricDisplay()
         Assert.assertEquals("Incorrect metric displayed for " + subFolderTile.get(2).getFolderName(), 10, subFolderTile.get(2).getMetricsCount());
     }
 
+    @Test
+    public void testBadMetricQuery()
+    {
+        // Set up a metric
+        String metricName = "BadMetric";
+        createQuery(getProjectName(), metricName, "targetedms", "SELECT * FROM AQCTest_Metric", null,  false);
+        ConfigureMetricsUIPage configureQCMetrics = goToDashboard().getQcPlotsWebPart().clickConfigureQCMetrics();
+        configureQCMetrics.addNewCustomMetric(Map.of(
+                ConfigureMetricsUIPage.CustomMetricProperties.metricName, metricName,
+                ConfigureMetricsUIPage.CustomMetricProperties.queryName, metricName,
+                ConfigureMetricsUIPage.CustomMetricProperties.yAxisLabel, "Label",
+                ConfigureMetricsUIPage.CustomMetricProperties.metricType, ConfigureMetricsUIPage.MetricType.Precursor.name()));
+
+        // Break the query and force a recaching
+        goToSchemaBrowser();
+        editQuerySource("targetedms", metricName).setSource("SELECT * FROM AQCTest_Metric_Bad").clickSaveExpectingError();
+        configureQCMetrics = goToDashboard().getQcPlotsWebPart().clickConfigureQCMetrics();
+        configureQCMetrics.clearMetricCache();
+
+        // Verify helpful error and then delete the bad metric
+        refresh();
+        waitForText("Failed to calculate metric values");
+        clickAndWait(Locator.linkWithText("View QC metrics table"));
+        DataRegionTable table = new DataRegionTable("query", getDriver());
+        table.setFilter("Name", "Equals", metricName);
+        table.checkCheckbox(0);
+        table.deleteSelectedRows();
+
+        goToDashboard().getQcPlotsWebPart().clickConfigureQCMetrics();
+        assertTextNotPresent(metricName);
+    }
+
     @Test
     public void testFixedDeviationFromMeanOption()
     {
         QCPlotsWebPart.MetricType metricType = QCPlotsWebPart.MetricType.TRANSITION_AREA;
-        goToProjectHome();
-        new PanoramaDashboard(this).getQcSummaryWebPart().clickMenuItem("Configure QC Metrics");
-        ConfigureMetricsUIPage configureQCMetrics = new ConfigureMetricsUIPage(this);
+        ConfigureMetricsUIPage configureQCMetrics = goToDashboard().getQcSummaryWebPart().clickConfigureQCMetrics();
 
         log("Validating the lower and upper limit inputs");
         configureQCMetrics.setFixedDeviationFromMean(metricType, "", null);
@@ -123,9 +154,7 @@ public void testFixedDeviationFromMeanOption()
     public void testFixedValueCutOffOption()
     {
         QCPlotsWebPart.MetricType metric = QCPlotsWebPart.MetricType.TRANSITION_MASS_ERROR;
-        goToProjectHome();
-        new PanoramaDashboard(this).getQcSummaryWebPart().clickMenuItem("Configure QC Metrics");
-        ConfigureMetricsUIPage configureQCMetrics = new ConfigureMetricsUIPage(this);
+        ConfigureMetricsUIPage configureQCMetrics = goToDashboard().getQcSummaryWebPart().clickConfigureQCMetrics();
 
         configureQCMetrics.setFixedValueCutOff(metric, "5", "-5");
         Assert.assertEquals("Incorrect error for upper bound < lower bound",
@@ -157,9 +186,7 @@ public void testFixedValueCutOffOption()
     public void testPlotOnlyOption()
     {
         QCPlotsWebPart.MetricType metric = QCPlotsWebPart.MetricType.ISOTOPE_DOTP;
-        goToProjectHome();
-        new PanoramaDashboard(this).getQcSummaryWebPart().clickMenuItem("Configure QC Metrics");
-        ConfigureMetricsUIPage configureQCMetrics = new ConfigureMetricsUIPage(this);
+        ConfigureMetricsUIPage configureQCMetrics = goToDashboard().getQcSummaryWebPart().clickConfigureQCMetrics();
         configureQCMetrics.setShowMetricNoOutlier(metric);
         configureQCMetrics.clickSave();
 
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java
index d81dc3de3..dfb2852af 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java
@@ -430,7 +430,7 @@ private void validateGuideSetStats(GuideSet gs) throws IOException, CommandExcep
     {
         for (GuideSetStats stats : gs.getStats())
         {
-
+            log("Testing guide set stats for " + stats.getMetricName());
             SelectRowsCommand cmd = new SelectRowsCommand("targetedms", "GuideSetStats_" + stats.getMetricName());
             cmd.setRequiredVersion(9.1);
             cmd.setColumns(Arrays.asList("GuideSetId", "TrainingStart", "TrainingEnd", "ReferenceEnd", "SeriesLabel", "NumRecords", "Mean", "StandardDev"));
@@ -549,13 +549,11 @@ private void verifyGuideSetSmallMoleculeStats(GuideSet gs) throws IOException, C
         String precursor = "C16,";
 
         gs.addStats(new GuideSetStats("retentionTime", 2, precursor, 0.7729333639144897, 9.424035327035906E-5));
-        gs.addStats(new GuideSetStats("peakArea", 2, precursor, 2.4647614E7, 5061170.5265));
         gs.addStats(new GuideSetStats("fwhm", 2, precursor, 0.023859419859945774, 0.0010710133238455678));
         gs.addStats(new GuideSetStats("fwb", 2, precursor, 0.11544176936149597, 0.012810408164340708));
         gs.addStats(new GuideSetStats("lhRatio", 0));
         gs.addStats(new GuideSetStats("transitionPrecursorRatio", 0, precursor, null, null));
         gs.addStats(new GuideSetStats("transitionArea", 2, precursor, 2.4647614E7, 5061170.5265));
-        gs.addStats(new GuideSetStats("precursorArea", 2, precursor, 0.0, 0.0));
 
         validateGuideSetStats(gs);
     }
diff --git a/webapp/TargetedMS/js/ParetoPlotPanel.js b/webapp/TargetedMS/js/ParetoPlotPanel.js
index fd96d4f9d..2f6d6152c 100644
--- a/webapp/TargetedMS/js/ParetoPlotPanel.js
+++ b/webapp/TargetedMS/js/ParetoPlotPanel.js
@@ -39,7 +39,7 @@ Ext4.define('LABKEY.targetedms.ParetoPlotPanel', {
 
         var parsed = JSON.parse(response.responseText);
 
-        if (Object.keys(parsed.sampleFiles).length === 0) {
+        if (!parsed.sampleFiles || Object.keys(parsed.sampleFiles).length === 0) {
             Ext4.get(this.plotDivId).update('<div class="tiledPlotPanel">No sample files loaded yet. Import some via Skyline, AutoQC, or the Data Pipeline tab here in Panorama.</div>');
             return;
         }
diff --git a/webapp/TargetedMS/js/QCSummaryPanel.js b/webapp/TargetedMS/js/QCSummaryPanel.js
index 5ef7b1894..99bf9d736 100644
--- a/webapp/TargetedMS/js/QCSummaryPanel.js
+++ b/webapp/TargetedMS/js/QCSummaryPanel.js
@@ -98,6 +98,7 @@ Ext4.define('LABKEY.targetedms.QCSummary', {
 
             }, this, false),
             failure: LABKEY.Utils.getCallbackWrapper(function (response) {
+                this.removeAll();
                 this.add(Ext4.create('Ext.Component', {
                     autoEl: 'span',
                     cls: 'labkey-error',
diff --git a/webapp/TargetedMS/js/QCTrendPlotPanel.js b/webapp/TargetedMS/js/QCTrendPlotPanel.js
index 8303fa15c..f22fbb0b9 100644
--- a/webapp/TargetedMS/js/QCTrendPlotPanel.js
+++ b/webapp/TargetedMS/js/QCTrendPlotPanel.js
@@ -1607,7 +1607,9 @@ Ext4.define('LABKEY.targetedms.QCTrendPlotPanel', {
 
     toggleGuideSetMsgDisplay : function() {
         var toolbarMsg = this.down('#GuideSetMessageToolBar');
-        toolbarMsg.up('toolbar').setVisible(this.enableBrushing);
+        if (toolbarMsg) {
+            toolbarMsg.up('toolbar').setVisible(this.enableBrushing);
+        }
     },
 
     highlightOutliersForClickedReplicate: function(plot, precursorInfo, replicateId) {