diff --git a/metatlas/plots/dill2plots.py b/metatlas/plots/dill2plots.py
index f0c1e3b3..98c18d2d 100644
--- a/metatlas/plots/dill2plots.py
+++ b/metatlas/plots/dill2plots.py
@@ -251,6 +251,7 @@ class adjust_rt_for_selected_compound(object):
     def __init__(self,
                  data,
                  msms_sorting_method=None,
+                 msms_radio_buttons=None,
                  include_lcmsruns=None,
                  exclude_lcmsruns=None,
                  include_groups=None,
@@ -308,6 +309,7 @@ def __init__(self,
         logger.debug("Initializing new instance of %s.", self.__class__.__name__)
         self.data = data
         self.msms_hits, _ = sp.sort_msms_hits(msms_hits, sorting_method=msms_sorting_method)
+        self.msms_radio_buttons = msms_radio_buttons
         self.color_me = or_default(color_me, [('black', '')])
         self.compound_idx = compound_idx
         self.width = width
@@ -509,24 +511,32 @@ def display_eic_data(self):
                                  picker=True, pickradius=5, color=color, label=label)
 
     def configure_flags(self):
-        default_peak = ['keep',
-                        'remove',
-                        'keep, unresolvable isomers',
-                        'keep, poor peak shape']
         
-        default_msms = ['no selection',
+        if self.msms_radio_buttons is None or self.msms_radio_buttons == 'new':
+            default_peak = ['keep','remove','keep, unresolvable isomers','keep, poor peak shape']
                         
-                        '-1.0, poor match, should remove',
-                        '0.0, no match or no MSMS collected',
-                        '0.5, partial or putative match of fragments',
-                        '1.0, good match',
-
-                        '0.5, co-isolated precursor, partial match',
-                        '1.0, co-isolated precursor, good match',
+            default_msms = ['no selection',
+                            '-1.0, poor match, should remove',
+                            '0.0, no match or no MSMS collected',
+                            '0.5, partial or putative match of fragments',
+                            '1.0, good match',
+                            '0.5, co-isolated precursor, partial match',
+                            '1.0, co-isolated precursor, good match',
+                            '0.5, single ion match, no evidence',
+                            '1.0, single ion match, ISTD/ref evidence']
+        elif self.msms_radio_buttons == 'old':
+            default_peak = ['keep','remove','unresolvable isomers','poor peak shape']
                         
-                        '0.5, single ion match, no evidence',
-                        '1.0, single ion match, ISTD/ref evidence']
-        
+            default_msms = ['no selection',
+                            '-1, bad match - should remove compound',
+                            '0, no ref match available or no MSMS collected',
+                            '0.5, partial match of fragments',
+                            '1, perfect match to internal reference library',
+                            '1, perfect match to external reference library',
+                            '1, co-isolated precursor but all reference ions are in sample spectrum']
+        else:
+            logger.warning('Unknown value for msms_radio_buttons: %s. Must use "old" or "new" or remove.', self.msms_radio_buttons)
+
         if self.peak_flags is None or self.peak_flags == '':
             self.peak_flags = default_peak
         if self.msms_flags is None or self.msms_flags == '':
diff --git a/metatlas/targeted/process.py b/metatlas/targeted/process.py
index 4a36f032..4de13157 100644
--- a/metatlas/targeted/process.py
+++ b/metatlas/targeted/process.py
@@ -76,6 +76,7 @@ def annotation_gui(
     peak_flags=None,
     msms_flags=None,
     msms_sorting_method: str = None,
+    msms_radio_buttons: str = None,
 ) -> Optional[dp.adjust_rt_for_selected_compound]:
     """
     Opens the interactive GUI for setting RT bounds and annotating peaks
@@ -96,6 +97,7 @@ def annotation_gui(
     return dp.adjust_rt_for_selected_compound(
         data,
         msms_sorting_method=msms_sorting_method,
+        msms_radio_buttons=msms_radio_buttons,
         msms_hits=data.hits,
         color_me=colors,
         compound_idx=compound_idx,
diff --git a/metatlas/tools/config.py b/metatlas/tools/config.py
index b74aeadc..1c4e032d 100644
--- a/metatlas/tools/config.py
+++ b/metatlas/tools/config.py
@@ -120,6 +120,7 @@ class AnalysisNotebookParameters(BaseNotebookParameters):
     slurm_execute: bool = False
     clear_cache: bool = False
     msms_sorting_method: Optional[str] = None
+    msms_radio_buttons: Optional[str] = None
     # these are populated from the workflow's RTAlignment if None
     google_folder: Optional[str] = None
     msms_refs: Optional[Path] = None
diff --git a/notebooks/reference/Targeted.ipynb b/notebooks/reference/Targeted.ipynb
index 86159317..03ced611 100644
--- a/notebooks/reference/Targeted.ipynb
+++ b/notebooks/reference/Targeted.ipynb
@@ -198,6 +198,11 @@
     "# If True, then include MSMS fragment ions in the output documents\n",
     "export_msms_fragment_ions = None\n",
     "\n",
+    "# One of 'old', 'new', or None. If 'old', use the old version of the\n",
+    "# MSMS (and MS) radio button selections in the GUI. If 'new' or None, use the \n",
+    "# new version of the MSMS (and MS) radio button selections in the GUI.\n",
+    "msms_radio_buttons = None\n",
+    "\n",
     "# Setting this to True will remove the cache of MSMS hits\n",
     "# if you don't see MSMS data for any of your compounds in RT adjuster GUI,\n",
     "# then you might want to try settings this to True. However, it will\n",
@@ -318,7 +323,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "agui = annotation_gui(data=metatlas_dataset, compound_idx=0, width=15, height=3, colors=analysis.parameters.line_colors, msms_sorting_method=analysis.parameters.msms_sorting_method)"
+    "agui = annotation_gui(data=metatlas_dataset, \n",
+    "                      compound_idx=0, width=15, height=3, \n",
+    "                      colors=analysis.parameters.line_colors, \n",
+    "                      msms_sorting_method=analysis.parameters.msms_sorting_method, \n",
+    "                      msms_radio_buttons=analysis.parameters.msms_radio_buttons)"
    ]
   },
   {