diff --git a/src/core/libmaven/PeakGroup.cpp b/src/core/libmaven/PeakGroup.cpp
index 3a97222ba3..c485faa708 100644
--- a/src/core/libmaven/PeakGroup.cpp
+++ b/src/core/libmaven/PeakGroup.cpp
@@ -862,8 +862,10 @@ vector<Scan*> PeakGroup::getFragmentationEvents()
         mzSample* sample = peak.getSample();
         if (sample == nullptr)
             continue;
-        if (sample->ms2ScanCount() == 0)
+        if (sample->ms2ScanCount() == 0
+            || sample->msMsType() != mzSample::MsMsType::DDA) {
             continue;
+        }
 
         mzSlice slice(minMz, maxMz, peak.rtmin, peak.rtmax);
         vector<Scan*> scans = sample->getFragmentationEvents(&slice);
diff --git a/src/core/libmaven/mzSample.cpp b/src/core/libmaven/mzSample.cpp
index e24ef7f0e6..321a436cdf 100644
--- a/src/core/libmaven/mzSample.cpp
+++ b/src/core/libmaven/mzSample.cpp
@@ -25,6 +25,7 @@ mzSample::mzSample() : _setName(""), injectionOrder(0)
     _id = -1;
     _numMS1Scans = 0;
     _numMS2Scans = 0;
+    _msMsType = MsMsType::None;
     maxMz = maxRt = 0;
     minMz = minRt = 0;
     isBlank = false;
diff --git a/src/core/libmaven/mzSample.h b/src/core/libmaven/mzSample.h
index 22c31ec6e2..4f9ab960b4 100644
--- a/src/core/libmaven/mzSample.h
+++ b/src/core/libmaven/mzSample.h
@@ -180,8 +180,13 @@ class mzLink
 */
 class mzSample
 {
+public:
+    enum class MsMsType {
+        DDA,
+        PRM,
+        None
+    };
 
-  public:
     /**
     * @brief Constructor for class mzSample
     */
@@ -681,6 +686,9 @@ class mzSample
 
     vector<float> getIntensityDistribution(int mslevel);
 
+    inline void setMsMsType(MsMsType msMsType) { _msMsType = msMsType; }
+    inline MsMsType msMsType() const { return _msMsType; }
+
     deque<Scan *> scans;
     string sampleName;
     string fileName;
@@ -728,6 +736,7 @@ class mzSample
     int _id;
     unsigned int _numMS1Scans;
     unsigned int _numMS2Scans;
+    MsMsType _msMsType;
 
     void sampleNaming(const char *filename);
     void checkSampleBlank(const char *filename);
diff --git a/src/gui/mzroll/eicwidget.cpp b/src/gui/mzroll/eicwidget.cpp
index ce04fa6645..e472080809 100644
--- a/src/gui/mzroll/eicwidget.cpp
+++ b/src/gui/mzroll/eicwidget.cpp
@@ -2120,7 +2120,11 @@ void EicWidget::addMS2Events(float mzmin, float mzmax)
 
     int count = 0;
     for (auto const& sample : samples) {
-        if (sample->ms1ScanCount() == 0) continue;
+        if (sample->ms1ScanCount() == 0
+            || sample->msMsType() != mzSample::MsMsType::DDA) {
+            continue;
+        }
+
         for (auto const& scan : sample->scans) {
             if (scan->mslevel == 2 && scan->precursorMz >= mzmin
                 && scan->precursorMz <= mzmax) {
diff --git a/src/gui/mzroll/mainwindow.cpp b/src/gui/mzroll/mainwindow.cpp
index d95dc3ab22..de127ab00c 100644
--- a/src/gui/mzroll/mainwindow.cpp
+++ b/src/gui/mzroll/mainwindow.cpp
@@ -605,6 +605,10 @@ using namespace mzUtils;
             SIGNAL(sampleLoaded()),
             this,
             SLOT(_warnIfNISTPolarityMismatch()));
+    connect(fileLoader,
+            &mzFileIO::sampleLoaded,
+            this,
+            &MainWindow::_confirmMsMsType);
 
 	connect(fileLoader,SIGNAL(sampleLoaded()), this, SLOT(setInjectionOrderFromTimeStamp()));
     connect(fileLoader,SIGNAL(sampleLoaded()),projectDockWidget, SLOT(updateSampleList()));
@@ -1543,8 +1547,6 @@ void MainWindow::setCompoundFocus(Compound* compound,
     if (fragPanel->isVisible())
         showFragmentationScans(mz);
 
-    QString compoundName(compound->name().c_str());
-
     if (compound)
         setUrl(compound);
 }
@@ -2143,6 +2145,38 @@ void MainWindow::_warnIfNISTPolarityMismatch()
     }
 }
 
+void MainWindow::_confirmMsMsType()
+{
+    QList<mzSample*> msMsSamples;
+    for (auto sample : samples) {
+        if (sample->ms1ScanCount() > 0 && sample->ms2ScanCount() > 0)
+            msMsSamples.append(sample);
+    }
+
+    if (msMsSamples.isEmpty())
+        return;
+
+    // TODO: add DIA when/if SWATH branch is merged
+    QStringList msMsTypes;
+    msMsTypes << tr("DDA") << tr("PRM");
+
+    QString type = QInputDialog::getItem(this,
+                                         tr("Select MS/MS type"),
+                                         tr("One or more samples have MS/MS "
+                                            "data. Please tell El-MAVEN the\n"
+                                            "acquisition type of this data:"),
+                                         msMsTypes,
+                                         0,
+                                         false);
+    for (auto sample : msMsSamples) {
+        if (type == "PRM") {
+            sample->setMsMsType(mzSample::MsMsType::PRM);
+        } else {
+            sample->setMsMsType(mzSample::MsMsType::DDA);
+        }
+    }
+}
+
 void MainWindow::setLastLoadedDatabase(QString filename)
 {
     QFileInfo fileInfo(filename);
@@ -4002,8 +4036,10 @@ void MainWindow::showFragmentationScans(float pmz)
         return;
     fragPanel->clearTree();
     for (auto sample : samples) {
-        if (sample->ms1ScanCount() == 0)
+        if (sample->ms1ScanCount() == 0
+            || sample->msMsType() != mzSample::MsMsType::DDA) {
             continue;
+        }
 
         for (auto scan : sample->scans) {
 	        if (scan->mslevel != 2) continue;
diff --git a/src/gui/mzroll/mainwindow.h b/src/gui/mzroll/mainwindow.h
index cdd4a814a8..b6b8a937d1 100644
--- a/src/gui/mzroll/mainwindow.h
+++ b/src/gui/mzroll/mainwindow.h
@@ -494,6 +494,7 @@ private Q_SLOTS:
 
     void _postProjectLoadActions();
     void _handleUnrecognizedProjectVersion(QString projectFilename);
+    void _confirmMsMsType();
 
 private:
     Controller* _controller;
diff --git a/src/gui/mzroll/peakdetectiondialog.cpp b/src/gui/mzroll/peakdetectiondialog.cpp
index 459622eb6f..4cbc2eeaf5 100644
--- a/src/gui/mzroll/peakdetectiondialog.cpp
+++ b/src/gui/mzroll/peakdetectiondialog.cpp
@@ -448,8 +448,9 @@ void PeakDetectionDialog::toggleFragmentation()
     auto iter = find_if(begin(samples),
                         end(samples),
                         [](mzSample* s) {
-                           return ((s->ms1ScanCount() > 0)
-                                   && (s->ms2ScanCount() > 0));
+                           return (s->ms1ScanCount() > 0
+                                   && s->ms2ScanCount() > 0
+                                   && s->msMsType() == mzSample::MsMsType::DDA);
                         });
     bool foundDda = iter != end(samples);