diff --git a/webapp/TargetedMS/js/QCPlotHelperBase.js b/webapp/TargetedMS/js/QCPlotHelperBase.js
index 11fb334b3..3a0ac0463 100644
--- a/webapp/TargetedMS/js/QCPlotHelperBase.js
+++ b/webapp/TargetedMS/js/QCPlotHelperBase.js
@@ -332,7 +332,7 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
 
                         Ext4.Object.each(this.guideSetDataMap, function(guideSetId, guideSetData) {
                             // for truncating out of range guideset data  find first index of plotDate ending at guideset.trainingEnd
-                            if (plotData.guideSetId === guideSetId && plotData.inGuideSetTrainingRange && guideSetData.TrainingEnd <= this.startDate) {
+                            if (plotData.guideSetId == guideSetId && plotData.inGuideSetTrainingRange && guideSetData.TrainingEnd <= this.startDate) {
                                 this.filterPoints[frag][plotData.MetricId]['filterPointsFirstIndex'] = j + 1;
                                 // ReferenceRangeSeries is used to separate series
                                 plotData['ReferenceRangeSeries'] = "GuideSet";
@@ -365,11 +365,18 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
         if (this.showExpRunRange && this.filterPoints) {
 
             for (let i = 0; i < plotDataRows.length; i++) {
-                Ext4.Object.each(this.filterPoints[plotDataRows[i].SeriesLabel], function (metricId, filterPointsData) {
+                const seriesPoints = this.filterPoints && this.filterPoints[plotDataRows[i].SeriesLabel];
+                if (!seriesPoints) {
+                    continue;
+                }
+                Ext4.Object.each(seriesPoints, function (metricId, filterPointsData) {
                     // no need to filter if less than 6 data points are present between reference end of guideset and startdate
                     if (filterPointsData['filterPointsFirstIndex'] && filterPointsData['filterPointsLastIndex']) {
                         if (filterPointsData['filterPointsLastIndex'] - filterPointsData['filterPointsFirstIndex'] < 6) {
-                            this.filterQCPoints = false;
+                            // Fewer than 6 out-of-range points for this series/metric, so there is nothing to truncate
+                            // for it. Flag only this entry rather than clearing the global this.filterQCPoints, so that
+                            // other series still truncate and the separator / guide-set line break still render.
+                            filterPointsData['skipTruncation'] = true;
                             // set the startDate field = acquired time of the 1st point of 5 points before the experiment run range
 
                             this.getStartDateField().setValue(this.formatDate(plotDataRows[i].data[filterPointsData['filterPointsFirstIndex']].AcquiredTime));
@@ -434,7 +441,7 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
         Ext4.Object.each(this.fragmentPlotData, function(label, fragmentData) {
             // traverse plotData backwards from firstIndex to lastIndex and
             // remove them from the array
-            if (this.filterQCPoints && this.filterPoints) {
+            if (this.filterQCPoints && this.filterPoints && this.filterPoints[label]) {
 
                 // when we're plotting two different metrics at the same time, then we
                 // have repeated dates (from oldest to newest for metric 1, and then oldest to newest for metric 2, all in the same array).
@@ -443,6 +450,9 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
                 const lab  = label;
 
                 filterPointsReversed.forEach(metricId => {
+                    if (this.filterPoints[lab][metricId]['skipTruncation']) {
+                        return; // too few out-of-range points for this series/metric to truncate
+                    }
                     let firstIndex = this.filterPoints[lab][metricId]['filterPointsFirstIndex'];
                     let lastIndex = this.filterPoints[lab][metricId]['filterPointsLastIndex'];
 
diff --git a/webapp/TargetedMS/js/QCTrendPlotPanel.js b/webapp/TargetedMS/js/QCTrendPlotPanel.js
index ec699977d..cc303f354 100644
--- a/webapp/TargetedMS/js/QCTrendPlotPanel.js
+++ b/webapp/TargetedMS/js/QCTrendPlotPanel.js
@@ -2325,8 +2325,10 @@ Ext4.define('LABKEY.targetedms.QCTrendPlotPanel', {
                         .attr('stroke', color).attr('stroke-opacity', 0.1)
                         .attr('fill', color).attr('fill-opacity', 0.1)
                         .append("title")
-                        .text(function (d) {
-                            return "Selected replicate: " + Ext4.String.htmlEncode(plot.data[d.EndIndex].ReplicateName);
+                        .text(function () {
+                            // 'data' is the already-matched point for this replicate, don't index plot.data by
+                            // seqValue (EndIndex), which breaks once out-of-range points have been truncated.
+                            return "Selected replicate: " + Ext4.String.htmlEncode(data.ReplicateName);
                         });
 
                 this.sendSvgElementToBack(plot, outlierRect);
@@ -2399,8 +2401,14 @@ Ext4.define('LABKEY.targetedms.QCTrendPlotPanel', {
                 var pointsData = precursorInfo.data;
                 var expDataArr = [];
 
-                for (var i = startIndex; i <= endIndex; i++) {
-                    expDataArr.push(pointsData[i].value);
+                // startIndex/endIndex are seqValues (x-axis positions), not array indices. Once out-of-range
+                // points are truncated, the array positions no longer line up with seqValue, so collect the
+                // experiment-range values by matching seqValue rather than indexing pointsData directly.
+                for (var i = 0; i < pointsData.length; i++) {
+                    if (pointsData[i].seqValue >= startIndex && pointsData[i].seqValue <= endIndex
+                            && pointsData[i].value !== undefined && pointsData[i].value !== null) {
+                        expDataArr.push(pointsData[i].value);
+                    }
                 }
 
                 var expMean = LABKEY.targetedms.PlotSettingsUtil.formatNumeric(LABKEY.vis.Stat.getMean(expDataArr));