diff --git a/downloads-generation/models_class1_pan_variants/GENERATE.sh b/downloads-generation/models_class1_pan_variants/GENERATE.sh
index 13d7aecb21190c574530318e718f6f2f876ff0de..7782d2fa1243440d46a00cfeb8ac38cd43284bf3 100755
--- a/downloads-generation/models_class1_pan_variants/GENERATE.sh
+++ b/downloads-generation/models_class1_pan_variants/GENERATE.sh
@@ -69,8 +69,8 @@ then
     python generate_hyperparameters.py hyperparameters.production.yaml compact_peptide > hyperparameters.compact_peptide.yaml
 fi
 
-#VARIANTS=( no_additional_ms_ms_only_0nm ms_only_0nm no_additional_ms_0nm 0nm no_additional_ms ms_only no_pretrain compact_peptide 34mer_sequence single_hidden_no_pretrain affinity_only )
-VARIANTS=( no_additional_ms_ms_only_0nm ms_only_0nm no_additional_ms_0nm 0nm no_additional_ms ms_only no_pretrain compact_peptide 34mer_sequence )
+#VARIANTS=( no_additional_ms_ms_only_0nm ms_only_0nm no_additional_ms_0nm 0nm no_additional_ms no_pretrain compact_peptide 34mer_sequence single_hidden_no_pretrain affinity_only )
+VARIANTS=( no_additional_ms_ms_only_0nm ms_only_0nm no_additional_ms_0nm 0nm no_additional_ms no_pretrain compact_peptide 34mer_sequence )
 
 for kind in "${VARIANTS[@]}"
 do
@@ -102,6 +102,7 @@ do
         python reassign_mass_spec_training_data.py \
             "$(mhcflurry-downloads path data_curated)/curated_training_data.no_additional_ms.csv.bz2" \
             --set-measurement-value 0 \
+            --drop-negative-ms \
             --ms-only \
             --out-csv "$TRAINING_DATA"
         HYPERPARAMETERS=hyperparameters.production.yaml
@@ -133,16 +134,11 @@ do
         python reassign_mass_spec_training_data.py \
             "$(mhcflurry-downloads path data_curated)/curated_training_data.mass_spec.csv.bz2" \
             --set-measurement-value 0 \
+            --drop-negative-ms \
             --out-csv "$TRAINING_DATA"
         HYPERPARAMETERS=hyperparameters.production.yaml
     fi
 
-    if [ "$kind" == "ms_only" ]
-    then
-        TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.mass_spec.csv.bz2"
-        HYPERPARAMETERS=hyperparameters.production.yaml
-    fi
-
     if [ "$kind" == "affinity_only" ]
     then
         TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.affinity.csv.bz2"
diff --git a/downloads-generation/models_class1_pan_variants/reassign_mass_spec_training_data.py b/downloads-generation/models_class1_pan_variants/reassign_mass_spec_training_data.py
index 158384193479a248c47f9e90434217f780fc3270..185eb75f6aef563cbb797dae0a5f4709184f22c0 100644
--- a/downloads-generation/models_class1_pan_variants/reassign_mass_spec_training_data.py
+++ b/downloads-generation/models_class1_pan_variants/reassign_mass_spec_training_data.py
@@ -11,6 +11,7 @@ parser = argparse.ArgumentParser(usage=__doc__)
 
 parser.add_argument("data", metavar="CSV", help="Training data")
 parser.add_argument("--ms-only", action="store_true", default=False)
+parser.add_argument("--drop-negative-ms", action="store_true", default=False)
 parser.add_argument("--set-measurement-value", type=float)
 parser.add_argument("--out-csv")
 
@@ -21,11 +22,13 @@ def go(args):
     df = pandas.read_csv(args.data)
     print(df)
 
-    bad = df.loc[
-        (df.measurement_kind == "mass_spec") &
-        (df.measurement_inequality != "<")
-    ]
-    assert len(bad) == 0, bad
+    if args.drop_negative_ms:
+        bad = df.loc[
+            (df.measurement_kind == "mass_spec") &
+            (df.measurement_inequality != "<")
+        ]
+        print("Dropping ", len(bad))
+        df = df.loc[~df.index.isin(bad.index)].copy()
 
     if args.ms_only:
         print("Filtering to MS only")