diff --git a/alphaquant/config/quant_reader_config.yaml b/alphaquant/config/quant_reader_config.yaml
index 0b253cda..ffb79612 100644
--- a/alphaquant/config/quant_reader_config.yaml
+++ b/alphaquant/config/quant_reader_config.yaml
@@ -863,6 +863,9 @@ spectronaut_fragion_ms1_gene:
       value: "True"
   use_iontree: True
   ml_level: CHARGE
+  variance_predictor_cols:
+    - EG.Cscore
+    - FG.ShapeQualityScore
 
 
 spectronaut_fragion_ms1_gene:
@@ -912,6 +915,9 @@ spectronaut_fragion_ms1_gene:
       value: 5.0
   use_iontree: True
   ml_level: CHARGE
+  variance_predictor_cols:
+    - EG.Cscore
+    - FG.ShapeQualityScore
 
 spectronaut_precursor_fragion_ms1:
   format: longtable
@@ -971,6 +977,9 @@ spectronaut_precursor_fragion_ms1:
       value: "True"
   use_iontree: True
   ml_level: CHARGE
+  variance_predictor_cols:
+    - EG.Cscore
+    - FG.ShapeQualityScore
 
 
 spectronaut_precursor_fragion_ms1:
@@ -1027,6 +1036,9 @@ spectronaut_precursor_fragion_ms1:
       value: 5.0
   use_iontree: True
   ml_level: CHARGE
+  variance_predictor_cols:
+    - EG.Cscore
+    - FG.ShapeQualityScore
 
 
 spectronaut_precursor_fragion_ms1_protein:
@@ -1083,6 +1095,9 @@ spectronaut_precursor_fragion_ms1_protein:
       value: 5.0
   use_iontree: True
   ml_level: CHARGE
+  variance_predictor_cols:
+    - EG.Cscore
+    - FG.ShapeQualityScore
 
 
 spectronaut_fragion_ms1_protein:
@@ -1132,6 +1147,9 @@ spectronaut_fragion_ms1_protein:
       value: 5.0
   use_iontree: True
   ml_level: CHARGE
+  variance_predictor_cols:
+    - EG.Cscore
+    - FG.ShapeQualityScore
   annotation_columns:
     - PG.Genes
 
@@ -1170,6 +1188,9 @@ spectronaut_fragion_protein:
       value: 5.0
   use_iontree: True
   ml_level: CHARGE
+  variance_predictor_cols:
+    - EG.Cscore
+    - FG.ShapeQualityScore
   annotation_columns:
     - PG.Genes
 
@@ -1342,8 +1363,25 @@ diaumpire_precursor_ms1:
   ion_cols:
    - Peptide Key
 
+fragpipe_precursor:
+  format: widetable
+  quant_pre_or_suffix: " Intensity"
+  protein_cols:
+   - Protein
+  ion_hierarchy:
+    sequence_int:
+      order: [SEQ, MOD, CHARGE]
+      mapping:
+        SEQ:
+          - Peptide Sequence
+        MOD:
+          - Modified Sequence
+        CHARGE:
+          - Charge
+  use_iontree: False
+  ml_level: SEQ
 
-fragpipe_precursors:
+fragpipe_modseq:
   format: widetable
   quant_pre_or_suffix: " Intensity"
   protein_cols:
@@ -1358,3 +1396,6 @@ fragpipe_precursors:
           - Modified Sequence
   use_iontree: False
   ml_level: SEQ
+
+
+
diff --git a/alphaquant/quant_reader/table_reformatter.py b/alphaquant/quant_reader/table_reformatter.py
index 9c3ebf0d..6dc17d8f 100644
--- a/alphaquant/quant_reader/table_reformatter.py
+++ b/alphaquant/quant_reader/table_reformatter.py
@@ -72,12 +72,11 @@ def merge_protein_cols_and_config_dict(
 
 def join_columns(df, columns, separator="_"):
     if len(columns) == 1:
-        return df[columns[0]].fillna("nan").infer_objects(copy=False).astype(str)
+        return df[columns[0]].fillna("nan").astype(str)
     else:
         return (
             df[columns]
             .fillna("nan")
-            .infer_objects(copy=False)
             .astype(str)
             .agg(separator.join, axis=1)
         )
diff --git a/alphaquant/tables/alphadia_reader.py b/alphaquant/tables/alphadia_reader.py
index f7f421ec..63be1412 100644
--- a/alphaquant/tables/alphadia_reader.py
+++ b/alphaquant/tables/alphadia_reader.py
@@ -26,17 +26,23 @@ def __init__(self, fragment_matrix_file: str):
 			fragment_matrix_file (str): Path to the fragment matrix file
 		"""
 
-		self.ml_info_file = aq_utils.get_progress_folder_filename(fragment_matrix_file, ".ml_info_table.tsv")
+		self.ml_info_file = aq_utils.get_progress_folder_filename(fragment_matrix_file, ".ml_info_table.tsv.zip")
+		self.old_ml_info_file = aq_utils.get_progress_folder_filename(fragment_matrix_file, ".ml_info_table.tsv")
 		self.input_file_reformat = aq_utils.get_progress_folder_filename(fragment_matrix_file, ".alphadia_fragion.aq_reformat.tsv", remove_extension=False)
 
 		precursor_file = os.path.join(os.path.dirname(fragment_matrix_file), "precursors.tsv")
 		self._precursor_df = aq_reader_utils.read_file(precursor_file, sep="\t")
 		self._precursor2quantID = self._precursor2quantid()
 
-		if not os.path.exists(self.ml_info_file):
+		if os.path.exists(self.old_ml_info_file) and not os.path.exists(self.ml_info_file):
+			self.ml_info_file = self.old_ml_info_file
+			LOGGER.info(f"ML info file already exists at {self.ml_info_file}")
+		elif not os.path.exists(self.ml_info_file):
 			LOGGER.info(f"Creating ML info file")
 			self.ml_info_df = self._define_ml_info_table()
-			self.ml_info_df.to_csv(self.ml_info_file, sep="\t", index=False)
+			archive_name = os.path.basename(self.ml_info_file).removesuffix(".zip")
+			compression = {"method": "zip", "archive_name": archive_name}
+			self.ml_info_df.to_csv(self.ml_info_file, sep="\t", index=False, compression=compression)
 		else:
 			LOGGER.info(f"ML info file already exists at {self.ml_info_file}")