diff --git a/directlfq/lfq_manager.py b/directlfq/lfq_manager.py
index 01dc418..fe5a12d 100644
--- a/directlfq/lfq_manager.py
+++ b/directlfq/lfq_manager.py
@@ -82,7 +82,7 @@ def get_outfile_basename(input_file, input_type_to_use, selected_proteins_file,
     return outfile_basename
 
 def save_protein_df(protein_df, outfile_basename):
-    protein_df.to_csv(f"{outfile_basename}.protein_intensities.tsv", sep = "\t")
+    protein_df.to_csv(f"{outfile_basename}.protein_intensities.tsv", sep = "\t", index = None)
 
 def save_ion_df(ion_df, outfile_basename):
     ion_df.to_csv(f"{outfile_basename}.ion_intensities.tsv", sep = "\t")
diff --git a/directlfq/utils.py b/directlfq/utils.py
index 11d1545..617edd3 100644
--- a/directlfq/utils.py
+++ b/directlfq/utils.py
@@ -272,7 +272,7 @@ def add_columns_to_lfq_results_table(lfq_results_df, input_file, columns_to_add)
     lfq_results_df_appended = pd.merge(lfq_results_df, input_df, left_on='protein', right_on=protein_column_input_table, how='left')
     length_after = len(lfq_results_df_appended.index)
 
-    lfq_results_df_appended = lfq_results_df_appended.set_index('protein')
+    #lfq_results_df_appended = lfq_results_df_appended.set_index('protein')
     
 
     assert length_before == length_after
diff --git a/test_data/.sync_journal.db-shm b/test_data/.sync_journal.db-shm
index 4a28bb0..0e68eb4 100644
Binary files a/test_data/.sync_journal.db-shm and b/test_data/.sync_journal.db-shm differ