diff --git a/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java b/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java
index 73d10893e..3a9000ac8 100644
--- a/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java
+++ b/api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java
@@ -33,6 +33,7 @@ public class QCMetricConfiguration implements Comparable<QCMetricConfiguration>
     private String _yAxisLabel;
     private Double _upperBound;
     private Double _lowerBound;
+    private String _annotationName;
 
     public int getId()
     {
@@ -164,6 +165,16 @@ public void setLowerBound(Double lowerBound)
         _lowerBound = lowerBound;
     }
 
+    public String getAnnotationName()
+    {
+        return _annotationName;
+    }
+
+    public void setAnnotationName(String annotationName)
+    {
+        _annotationName = annotationName;
+    }
+
     public JSONObject toJSON(){
         JSONObject jsonObject = new JSONObject();
         jsonObject.put("id", _id);
@@ -195,6 +206,9 @@ public JSONObject toJSON(){
         if (_upperBound != null) {
             jsonObject.put("upperBound", _upperBound);
         }
+        if (_annotationName != null) {
+            jsonObject.put("annotationName", _annotationName);
+        }
 
         return jsonObject;
     }
diff --git a/resources/queries/targetedms/qcMetricsConfig.sql b/resources/queries/targetedms/qcMetricsConfig.sql
index d1f1248ef..bb5d5082d 100644
--- a/resources/queries/targetedms/qcMetricsConfig.sql
+++ b/resources/queries/targetedms/qcMetricsConfig.sql
@@ -30,7 +30,8 @@ SELECT
        qmc.MaxTimeValue,
        qmc.TimeValueOption,
        qmc.TraceName,
-       qmc.YAxisLabel
+       qmc.YAxisLabel,
+       qmc.AnnotationName
 FROM
       qcmetricconfiguration qmc
 FULL JOIN   qcenabledmetrics qem
diff --git a/resources/schemas/dbscripts/postgresql/targetedms-26.007-26.008.sql b/resources/schemas/dbscripts/postgresql/targetedms-26.007-26.008.sql
new file mode 100644
index 000000000..c00cd2a66
--- /dev/null
+++ b/resources/schemas/dbscripts/postgresql/targetedms-26.007-26.008.sql
@@ -0,0 +1 @@
+ALTER TABLE targetedms.QCMetricConfiguration ADD COLUMN AnnotationName VARCHAR(200);
diff --git a/resources/schemas/targetedms.xml b/resources/schemas/targetedms.xml
index 8fddaf6bf..0676c5526 100644
--- a/resources/schemas/targetedms.xml
+++ b/resources/schemas/targetedms.xml
@@ -1358,6 +1358,7 @@
             <column columnName="TimeValueOption"/>
             <column columnName="TraceName"/>
             <column columnName="YAxisLabel"/>
+            <column columnName="AnnotationName"/>
         </columns>
     </table>
     <table tableName="QCMetricExclusion" tableDbType="TABLE">
diff --git a/resources/views/configureQCMetric.html b/resources/views/configureQCMetric.html
index 9a608a2c5..d8dbc8b0c 100644
--- a/resources/views/configureQCMetric.html
+++ b/resources/views/configureQCMetric.html
@@ -59,11 +59,14 @@
             });
 
             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" style="margin-right: 20px;">Add New Trace Metric</button>' +
+                    '<div style="display:flex;flex-wrap:wrap;gap:8px;">' +
+                    '<button type="button" class="labkey-button primary" id="saveButton">Save</button>' +
+                    '<button type="button" class="labkey-button" id="cancelButton">Cancel</button>' +
+                    '<button type="button" class="labkey-button" id="createNewCustomMetricButton">Add New Custom Metric</button>' +
+                    '<button type="button" class="labkey-button" id="createNewTraceMetricButton">Add New Trace Metric</button>' +
+                    '<button type="button" class="labkey-button" id="createNewAnnotationMetricButton">Add Annotation-Backed Metric</button>' +
                     '<button type="button" class="labkey-button" id="clearCacheButton">Clear Cached Metric Values</button>' +
+                    '</div>' +
                     '</form><br>Edits to queries backing existing custom metrics require a manual cache clearing to display the updated results.</p>';
 
             jQuery('#qcMetricsTable').html(qcMetricsTable);
@@ -80,7 +83,10 @@
                 LABKEY.internal.ConfigureQCMetrics.addNewMetric('custom');
             });
             jQuery('#createNewTraceMetricButton').click(function() {
-                LABKEY.internal.ConfigureQCMetrics.addNewMetric('trace')
+                LABKEY.internal.ConfigureQCMetrics.addNewMetric('trace');
+            });
+            jQuery('#createNewAnnotationMetricButton').click(function() {
+                LABKEY.internal.ConfigureQCMetrics.addNewMetric('annotation');
             });
             jQuery('#clearCacheButton').click(function() {
                 jQuery('#qcMetricsError').text('Clearing cached metrics...');
@@ -169,7 +175,10 @@
 
                 const op = 'update';
                 if (clickedQcMetricConfig.TraceName) {
-                    LABKEY.internal.ConfigureQCMetrics.showTraceMetricWindow(op, clickedQcMetricConfig)
+                    LABKEY.internal.ConfigureQCMetrics.showTraceMetricWindow(op, clickedQcMetricConfig);
+                }
+                else if (clickedQcMetricConfig.AnnotationName) {
+                    LABKEY.internal.ConfigureQCMetrics.showAnnotationMetricWindow(op, clickedQcMetricConfig);
                 }
                 else {
                     LABKEY.internal.ConfigureQCMetrics.showCustomMetricWindow(op, clickedQcMetricConfig);
@@ -242,13 +251,27 @@
                 });
             },
 
+            showAnnotationMetricWindow: function (op, clickedMetric) {
+                const windowConfig = {
+                    parent: this,
+                    operation: op
+                };
+                if (clickedMetric) {
+                    windowConfig.metric = clickedMetric;
+                }
+                Panorama.Window.AddAnnotationMetricWindow.show(windowConfig);
+            },
+
             addNewMetric: function (metricType) {
                 const op = 'insert';
                 if (metricType === 'custom') {
                     this.showCustomMetricWindow(op);
                 }
                 else if (metricType === 'trace') {
-                    this.showTraceMetricWindow(op)
+                    this.showTraceMetricWindow(op);
+                }
+                else if (metricType === 'annotation') {
+                    this.showAnnotationMetricWindow(op);
                 }
             },
 
diff --git a/resources/views/configureQCMetric.view.xml b/resources/views/configureQCMetric.view.xml
index d10619e34..69c26d2dd 100644
--- a/resources/views/configureQCMetric.view.xml
+++ b/resources/views/configureQCMetric.view.xml
@@ -7,6 +7,7 @@
         <dependency path="Ext4"/>
         <dependency path="PanoramaPremium/window/AddNewMetricWindow.js"/>
         <dependency path="PanoramaPremium/window/AddNewTraceMetricWindow.js"/>
+        <dependency path="PanoramaPremium/window/AddNewAnnotationMetricWindow.js"/>
         <dependency path="TargetedMS/js/misc.js"/>
     </dependencies>
 </view>
\ No newline at end of file
diff --git a/resources/web/PanoramaPremium/window/AddNewAnnotationMetricWindow.js b/resources/web/PanoramaPremium/window/AddNewAnnotationMetricWindow.js
new file mode 100644
index 000000000..fc762eed0
--- /dev/null
+++ b/resources/web/PanoramaPremium/window/AddNewAnnotationMetricWindow.js
@@ -0,0 +1,226 @@
+/*
+ * Copyright (c) 2025 LabKey Corporation. All rights reserved. No portion of this work may be reproduced in
+ * any form or by any electronic or mechanical means without written permission from LabKey Corporation.
+ */
+
+(function($) {
+    window.Panorama = window.Panorama || {};
+    window.Panorama.Window = window.Panorama.Window || {};
+
+    const DIALOG_ID = 'lk-annotation-metric-dialog';
+    let _config = null;
+    let _allAnnotations = [];
+
+    function closeDialog() {
+        $('#' + DIALOG_ID).remove();
+    }
+
+    function showError(msg) {
+        $('#lk-annotation-metric-error').text(msg).show();
+    }
+
+    function clearErrors() {
+        $('#lk-annotation-metric-error').hide().text('');
+        $('#lk-annotation-metric-name, #lk-annotation-metric-ylabel, #lk-annotation-name-select')
+            .css('border-color', '');
+    }
+
+    function markInvalid($field) {
+        $field.css('border-color', 'red');
+    }
+
+    function validate() {
+        clearErrors();
+        let isValid = true;
+
+        if (!$('#lk-annotation-metric-name').val().trim()) {
+            markInvalid($('#lk-annotation-metric-name'));
+            isValid = false;
+        }
+        if (!$('#lk-annotation-metric-ylabel').val().trim()) {
+            markInvalid($('#lk-annotation-metric-ylabel'));
+            isValid = false;
+        }
+        if (!$('#lk-annotation-name-select').val()) {
+            markInvalid($('#lk-annotation-name-select'));
+            isValid = false;
+        }
+
+        if (!isValid) {
+            showError('Please fill in all required fields.');
+        }
+        return isValid;
+    }
+
+    function getAnnotationTarget() {
+        return $('input[name="annotationType"]:checked').val() === 'precursor'
+            ? 'precursor_result'
+            : 'replicate';
+    }
+
+    function getFilteredAnnotations() {
+        const target = getAnnotationTarget();
+        const seen = {};
+        const result = [];
+        _allAnnotations.forEach(function(row) {
+            const targets = (row['Targets'] || '').split(',').map(function(s) { return s.trim(); });
+            if (targets.indexOf(target) >= 0 && !seen[row['Name']]) {
+                seen[row['Name']] = true;
+                result.push(row['Name']);
+            }
+        });
+        result.sort();
+        return result;
+    }
+
+    function refreshAnnotationsSelect() {
+        const $select = $('#lk-annotation-name-select');
+        const currentVal = $select.val();
+        $select.empty().append($('<option>').val('').text('-- Select annotation --'));
+        getFilteredAnnotations().forEach(function(name) {
+            $select.append($('<option>').val(name).text(name));
+        });
+
+        const metric = _config && _config.metric;
+        if (_config.operation === 'update' && metric && metric.AnnotationName) {
+            $select.val(metric.AnnotationName);
+        } else if (currentVal) {
+            $select.val(currentVal);
+        }
+    }
+
+    function checkMetricNameExists(metricName, callback) {
+        const filterArray = [LABKEY.Filter.create('Name', metricName, LABKEY.Filter.Types.EQUAL)];
+        if (_config.operation === 'update' && _config.metric) {
+            filterArray.push(LABKEY.Filter.create('id', _config.metric.id, LABKEY.Filter.Types.NOT_EQUAL));
+        }
+        LABKEY.Query.selectRows({
+            containerPath: LABKEY.container.id,
+            schemaName: 'targetedms',
+            queryName: 'qcmetricconfiguration',
+            filterArray: filterArray,
+            success: function(data) { callback(data.rows.length > 0); },
+            failure: function() { callback(false); }
+        });
+    }
+
+    function save() {
+        if (!validate()) return;
+
+        const metricName = $('#lk-annotation-metric-name').val().trim();
+        checkMetricNameExists(metricName, function(exists) {
+            if (exists) {
+                showError('A metric with the name "' + LABKEY.Utils.encodeHtml(metricName) + '" already exists. Please choose a different name.');
+                markInvalid($('#lk-annotation-metric-name'));
+                return;
+            }
+
+            const newMetric = {
+                Name: metricName,
+                QueryName: 'QCAnnotationMetric',
+                YAxisLabel: $('#lk-annotation-metric-ylabel').val().trim(),
+                PrecursorScoped: $('input[name="annotationType"]:checked').val() === 'precursor',
+                AnnotationName: $('#lk-annotation-name-select').val()
+            };
+            if (_config.operation === 'update') {
+                newMetric.id = _config.metric.id;
+            }
+
+            LABKEY.Query.saveRows({
+                containerPath: LABKEY.container.id,
+                commands: [{ schemaName: 'targetedms', queryName: 'qcmetricconfiguration', command: _config.operation, rows: [newMetric] }],
+                method: 'POST',
+                success: function() { window.location.reload(); },
+                failure: function(response) {
+                    showError((response && (response.exception || response.message)) || 'Error saving metric');
+                }
+            });
+        });
+    }
+
+    function deleteMetric() {
+        if (!confirm('This will delete the "' + _config.metric.name + '" metric. Are you sure?')) return;
+
+        LABKEY.Query.saveRows({
+            containerPath: LABKEY.container.id,
+            commands: [
+                { schemaName: 'targetedms', queryName: 'qcenabledmetrics', command: 'delete', rows: [{ metric: _config.metric.id }] },
+                { schemaName: 'targetedms', queryName: 'qcmetricconfiguration', command: 'delete', rows: [{ id: _config.metric.id }] }
+            ],
+            method: 'POST',
+            success: function() { window.location.reload(); },
+            failure: function(response) {
+                showError((response && (response.exception || response.message)) || 'Error deleting metric');
+            }
+        });
+    }
+
+    function buildDialogHtml() {
+        const op = _config.operation;
+        const metric = _config.metric || {};
+        const isPrecursor = op === 'update' && metric.PrecursorScoped;
+        const title = op === 'insert' ? 'Add Annotation-Backed Metric' : 'Edit Annotation-Backed Metric';
+
+        return '<div id="' + DIALOG_ID + '" style="position:fixed;top:0;left:0;width:100%;height:100%;background:rgba(0,0,0,0.5);z-index:9999;display:flex;align-items:center;justify-content:center;">'
+            + '<div class="x4-window x4-window-default" style="min-width:480px;max-width:580px;">'
+            +   '<div class="x4-window-header x4-window-header-default x4-window-header-default-top" style="padding:4px 8px;border:none;">'
+            +     '<p class="x4-window-header-text-container-default" style="font-size:14px;margin:0;">' + LABKEY.Utils.encodeHtml(title) + '</p>'
+            +   '</div>'
+            +   '<div class="x4-window-body" style="background:white;padding:10px 12px;">'
+            +     '<table style="border-collapse:collapse;width:100%;">'
+            +       '<tr><td style="padding:5px 10px 5px 0;white-space:nowrap;"><label for="lk-annotation-metric-name">Metric Name *</label></td>'
+            +           '<td style="padding:5px 0;"><input type="text" id="lk-annotation-metric-name" style="width:100%;box-sizing:border-box;" value="' + LABKEY.Utils.encodeHtml(metric.name || '') + '"/></td></tr>'
+            +       '<tr><td style="padding:5px 10px 5px 0;white-space:nowrap;"><label for="lk-annotation-metric-ylabel">Y-Axis Label *</label></td>'
+            +           '<td style="padding:5px 0;"><input type="text" id="lk-annotation-metric-ylabel" style="width:100%;box-sizing:border-box;" value="' + LABKEY.Utils.encodeHtml(metric.YAxisLabel || '') + '"/></td></tr>'
+            +       '<tr><td style="padding:5px 10px 5px 0;white-space:nowrap;">Annotation Type</td>'
+            +           '<td style="padding:5px 0;">'
+            +             '<label style="margin-right:16px;"><input type="radio" name="annotationType" value="replicate"' + (!isPrecursor ? ' checked' : '') + '> Replicate</label>'
+            +             '<label><input type="radio" name="annotationType" value="precursor"' + (isPrecursor ? ' checked' : '') + '> Precursor</label>'
+            +           '</td></tr>'
+            +       '<tr><td style="padding:5px 10px 5px 0;white-space:nowrap;"><label for="lk-annotation-name-select">Annotation *</label></td>'
+            +           '<td style="padding:5px 0;"><select id="lk-annotation-name-select" style="width:100%;box-sizing:border-box;"><option value="">Loading...</option></select></td></tr>'
+            +     '</table>'
+            +     '<div id="lk-annotation-metric-error" class="labkey-error" style="display:none;margin-top:8px;"></div>'
+            +     '<div style="margin-top:12px;text-align:right;">'
+            +       '<button type="button" class="labkey-button" id="lk-annotation-metric-cancel">Cancel</button>'
+            +       (op === 'update' ? ' <button type="button" class="labkey-button" id="lk-annotation-metric-delete">Delete</button>' : '')
+            +       ' <button type="button" class="labkey-button primary" id="lk-annotation-metric-save">Save</button>'
+            +     '</div>'
+            +   '</div>'
+            + '</div>'
+            + '</div>';
+    }
+
+    window.Panorama.Window.AddAnnotationMetricWindow = {
+        show: function(config) {
+            _config = config;
+            _allAnnotations = [];
+
+            $('#' + DIALOG_ID).remove();
+            $('body').append(buildDialogHtml());
+
+            $('#lk-annotation-metric-cancel').on('click', closeDialog);
+            $('#lk-annotation-metric-save').on('click', save);
+            if (config.operation === 'update') {
+                $('#lk-annotation-metric-delete').on('click', deleteMetric);
+            }
+            $('input[name="annotationType"]').on('change', refreshAnnotationsSelect);
+
+            // close on overlay click
+            $('#' + DIALOG_ID).on('click', function(e) {
+                if (e.target === this) closeDialog();
+            });
+
+            LABKEY.Query.selectRows({
+                schemaName: 'targetedms',
+                queryName: 'AnnotationSettings',
+                columns: ['Name', 'Targets', 'Type'],
+                filterArray: [LABKEY.Filter.create('Type', 'number', LABKEY.Filter.Types.EQUAL)],
+                success: function(data) {
+                    _allAnnotations = data.rows || [];
+                    refreshAnnotationsSelect();
+                }
+            });
+        }
+    };
+})(jQuery);
diff --git a/src/org/labkey/targetedms/TargetedMSModule.java b/src/org/labkey/targetedms/TargetedMSModule.java
index 581f67f52..d4739e31e 100644
--- a/src/org/labkey/targetedms/TargetedMSModule.java
+++ b/src/org/labkey/targetedms/TargetedMSModule.java
@@ -231,7 +231,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 26.006;
+        return 26.008;
     }
 
     @Override
diff --git a/src/org/labkey/targetedms/outliers/OutlierGenerator.java b/src/org/labkey/targetedms/outliers/OutlierGenerator.java
index f2c42bbdb..f0e8c55be 100644
--- a/src/org/labkey/targetedms/outliers/OutlierGenerator.java
+++ b/src/org/labkey/targetedms/outliers/OutlierGenerator.java
@@ -100,6 +100,30 @@ private String getEachSeriesTypePlotDataSql(QCMetricConfiguration configuration)
             sql.append(" WHERE metric = ").append(configuration.getId());
             sql.append(")");
         }
+        else if (configuration.getAnnotationName() != null)
+        {
+            // annotation-backed metrics: escape the annotation name for SQL string literal
+            String escapedName = configuration.getAnnotationName().replace("'", "''");
+            if (configuration.isPrecursorScoped())
+            {
+                sql.append("(SELECT pcia.PrecursorChromInfoId, pci.SampleFileId,");
+                sql.append(" pcia.Name AS SeriesLabel,");
+                sql.append(" CAST(pcia.Value AS REAL) AS MetricValue, ").append(configuration.getId()).append(" AS MetricId");
+                sql.append(" FROM ").append(schemaName).append(".PrecursorChromInfoAnnotation pcia");
+                sql.append(" INNER JOIN ").append(schemaName).append(".PrecursorChromInfo pci ON pcia.PrecursorChromInfoId = pci.Id");
+                sql.append(" WHERE pcia.Name = '").append(escapedName).append("')");
+            }
+            else
+            {
+                sql.append("(SELECT 0 AS PrecursorChromInfoId, sf.Id AS SampleFileId,");
+                sql.append(" ra.Name AS SeriesLabel,");
+                sql.append(" CAST(ra.Value AS REAL) AS MetricValue, ").append(configuration.getId()).append(" AS MetricId");
+                sql.append(" FROM ").append(schemaName).append(".ReplicateAnnotation ra");
+                sql.append(" INNER JOIN ").append(schemaName).append(".Replicate r ON ra.ReplicateId = r.Id");
+                sql.append(" INNER JOIN ").append(schemaName).append(".SampleFile sf ON sf.ReplicateId = r.Id");
+                sql.append(" WHERE ra.Name = '").append(escapedName).append("')");
+            }
+        }
         else
         {
             sql.append("(SELECT PrecursorChromInfoId, SampleFileId, ");
diff --git a/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java b/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java
index b87419916..358df607d 100644
--- a/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java
+++ b/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java
@@ -16,6 +16,7 @@ public class ConfigureMetricsUIPage extends PortalBodyPanel
 {
 
     public static final String ADD_NEW_CUSTOM_METRIC = "Add New Custom Metric";
+    public static final String ADD_NEW_ANNOTATION_METRIC = "Add Annotation-Backed Metric";
 
     public ConfigureMetricsUIPage(WebDriver driver)
     {
@@ -134,6 +135,42 @@ public void addNewTraceMetric(Map<TraceMetricProperties, String> traceProperties
         editTraceMetricValues(metricWindow, traceProperties, duplicateNameErrorExpected);
     }
 
+    public void addNewAnnotationMetric(Map<AnnotationMetricProperties, String> metricProperties, boolean duplicateNameErrorExpected)
+    {
+        click(Locator.tagWithText("button", ADD_NEW_ANNOTATION_METRIC));
+        waitForAnnotationDialog();
+        fillAnnotationForm(metricProperties);
+        if (duplicateNameErrorExpected)
+        {
+            click(Locator.id("lk-annotation-metric-save"));
+            String metricName = metricProperties.get(AnnotationMetricProperties.metricName);
+            assertTextPresent("A metric with the name \"" + metricName + "\" already exists. Please choose a different name.");
+            click(Locator.id("lk-annotation-metric-cancel"));
+        }
+        else
+        {
+            clickAndWait(Locator.id("lk-annotation-metric-save"));
+        }
+    }
+
+    public void editAnnotationMetric(String metric, Map<AnnotationMetricProperties, String> metricProperties)
+    {
+        waitAndClick(Locator.linkWithText(metric));
+        waitForAnnotationDialog();
+        fillAnnotationForm(metricProperties);
+        clickAndWait(Locator.id("lk-annotation-metric-save"));
+    }
+
+    public void deleteAnnotationMetric(String metric)
+    {
+        waitAndClick(Locator.linkWithText(metric));
+        waitForAnnotationDialog();
+        click(Locator.id("lk-annotation-metric-delete"));
+        acceptAlert();
+        waitForPage();
+        waitForElementToDisappear(Locator.linkWithText(metric));
+    }
+
     public void editMetric(String metric, Map<CustomMetricProperties, String> metricProperties)
     {
         Window<?> metricWindow = openForEdit(metric);
@@ -215,6 +252,28 @@ else if (prop.formLabel != null)
         }
     }
 
+    private void waitForAnnotationDialog()
+    {
+        waitForElement(Locator.id("lk-annotation-metric-dialog"));
+        waitForElement(Locator.tagWithText("option", "-- Select annotation --"));
+    }
+
+    private void fillAnnotationForm(Map<AnnotationMetricProperties, String> props)
+    {
+        if (props.containsKey(AnnotationMetricProperties.metricName))
+            setFormElement(Locator.id("lk-annotation-metric-name"), props.get(AnnotationMetricProperties.metricName));
+        if (props.containsKey(AnnotationMetricProperties.yAxisLabel))
+            setFormElement(Locator.id("lk-annotation-metric-ylabel"), props.get(AnnotationMetricProperties.yAxisLabel));
+        if (props.containsKey(AnnotationMetricProperties.annotationType))
+            click(Locator.css("input[name='annotationType'][value='" + props.get(AnnotationMetricProperties.annotationType) + "']"));
+        if (props.containsKey(AnnotationMetricProperties.annotationName))
+        {
+            String annotationName = props.get(AnnotationMetricProperties.annotationName);
+            waitForElement(Locator.tagWithText("option", annotationName));
+            selectOptionByText(Locator.id("lk-annotation-name-select"), annotationName);
+        }
+    }
+
     private void duplicateNameErrorExpected(String metricName)
     {
         click(Ext4Helper.Locators.ext4Button("Save"));
@@ -251,6 +310,14 @@ public enum CustomMetricProperties
         }
     }
 
+    public enum AnnotationMetricProperties
+    {
+        metricName,
+        yAxisLabel,
+        annotationType,   // "replicate" or "precursor"
+        annotationName
+    }
+
     public enum TraceMetricProperties
     {
         metricName(null, false),
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
index e34b17b0f..6095cfd79 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
@@ -23,7 +23,7 @@
  * Tests the QC metric configuration UI and verifies settings propagate consistently across folder hierarchies.
  */
 @Category({})
-@BaseWebDriverTest.ClassTimeout(minutes = 5)
+@BaseWebDriverTest.ClassTimeout(minutes = 15)
 public class TargetedMSQCConfigureMetricTest extends TargetedMSPremiumTest
 {
     private final static String SUBFOLDER_1 = "QC Subfolder 1";
@@ -206,6 +206,54 @@ public void testPlotOnlyOption()
         verifyOutlierCount(replicate, metric, "N/A");
     }
 
+    @Test
+    public void testAnnotationBackedMetric()
+    {
+        String subfolderName = "AnnotationMetricsFolder";
+        String metricName = "Annotation Metric R Squared";
+        String yAxisLabel = "R Squared";
+        String updatedYAxisLabel = "Updated R Squared";
+
+        log("Create subfolder and import data with numeric precursor_result annotations");
+        setupSubfolder(getProjectName(), subfolderName, FolderType.QC);
+        importData(ISOTOPOLOGUE_FILE_ANNOTATED);
+        navigateToFolder(getProjectName(), subfolderName);
+
+        log("Add annotation-backed metric backed by the RSquared precursor annotation");
+        ConfigureMetricsUIPage configureQCMetrics = goToDashboard().getQcSummaryWebPart().clickConfigureQCMetrics();
+        configureQCMetrics.addNewAnnotationMetric(Map.of(
+                ConfigureMetricsUIPage.AnnotationMetricProperties.metricName, metricName,
+                ConfigureMetricsUIPage.AnnotationMetricProperties.yAxisLabel, yAxisLabel,
+                ConfigureMetricsUIPage.AnnotationMetricProperties.annotationType, "precursor",
+                ConfigureMetricsUIPage.AnnotationMetricProperties.annotationName, "RSquared"), false);
+
+        log("Verify metric appears in configure QC metrics table");
+        waitForElement(Locator.linkWithText(metricName));
+
+        goToDashboard();
+        log("Verify metric appears in QC plots dropdown");
+        QCPlotsWebPart qcPlotsWebPart = new PanoramaDashboard(this).getQcPlotsWebPart();
+        Assert.assertTrue("Annotation-backed metric should appear in QC plots dropdown",
+                verifyMetricIsPresent(qcPlotsWebPart, metricName));
+
+        log("Test that a duplicate metric name is rejected");
+        configureQCMetrics = goToDashboard().getQcSummaryWebPart().clickConfigureQCMetrics();
+        configureQCMetrics.addNewAnnotationMetric(Map.of(
+                ConfigureMetricsUIPage.AnnotationMetricProperties.metricName, metricName,
+                ConfigureMetricsUIPage.AnnotationMetricProperties.yAxisLabel, "Duplicate Label",
+                ConfigureMetricsUIPage.AnnotationMetricProperties.annotationType, "precursor",
+                ConfigureMetricsUIPage.AnnotationMetricProperties.annotationName, "RSquared"), true);
+
+        log("Edit the annotation-backed metric's y-axis label (still on same page after cancel)");
+        configureQCMetrics.editAnnotationMetric(metricName, Map.of(
+                ConfigureMetricsUIPage.AnnotationMetricProperties.yAxisLabel, updatedYAxisLabel));
+
+        log("Delete the annotation-backed metric");
+        configureQCMetrics = goToDashboard().getQcSummaryWebPart().clickConfigureQCMetrics();
+        configureQCMetrics.deleteAnnotationMetric(metricName);
+        assertTextNotPresent(metricName);
+    }
+
     private void verifyOutlierCount(String replicate, QCPlotsWebPart.MetricType metricType, String count)
     {
         QCSummaryWebPart qcSummaryWebPart = new PanoramaDashboard(this).getQcSummaryWebPart();