diff --git a/mhcflurry/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
index 9a8aaecc38f10b90594551c52d4d17cd48adf7e2..b621a4fcc92bd7ff8977eb4b33b44a11eebddc3a 100644
--- a/mhcflurry/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -1120,15 +1120,14 @@ class Class1AffinityPredictor(object):
                 masked_allele_encoding = AlleleEncoding(
                     df.normalized_allele,
                     borrow_from=master_allele_encoding)
-                masked_peptides = peptides
+                masked_peptides = EncodableSequences.create(peptides)
             elif mask.sum() > 0:
                 row_slice = mask
                 masked_allele_encoding = AlleleEncoding(
                     df.loc[mask].normalized_allele,
                     borrow_from=master_allele_encoding)
-                masked_peptides = peptides.sequences[mask]
-
-            masked_peptides = EncodableSequences.create(masked_peptides)
+                masked_peptides = EncodableSequences.create(
+                    peptides.sequences[mask])
 
             if row_slice is not None:
                 # The following line is a performance optimization that may be