diff --git a/alphaquant/cluster/cluster_missingval.py b/alphaquant/cluster/cluster_missingval.py
index f1d2763a..6dfa12b4 100644
--- a/alphaquant/cluster/cluster_missingval.py
+++ b/alphaquant/cluster/cluster_missingval.py
@@ -8,6 +8,42 @@
 
 PVALUE_THRESHOLD_FOR_INTENSITY_BASED_COUNTING = 0.1
 
+# Determines at which level missing value testing is performed.
+# Set once based on tree structure, then reused.
+MISSINGVAL_TEST_LEVEL = None
+
+
+def _determine_missingval_test_level(root_node):
+    """Determine the appropriate level for missing value statistical testing.
+
+    Scenarios:
+    1) "mod_seq_charge" exists in tree -> test at mod_seq_charge level
+    2) "mod_seq" is one level above leaves -> test at base ion level
+    3) "seq" is one level above leaves -> test at base ion level
+    4) "gene" is one level above leaves -> test at base ion level
+    """
+    # Check if mod_seq_charge nodes exist (fragment-level data)
+    mod_seq_charge_nodes = anytree.search.findall(root_node, filter_=lambda node: node.type == "mod_seq_charge")
+    if len(mod_seq_charge_nodes) > 0:
+        # Scenario 1: fragment-level data — everything below mod_seq_charge is collapsed to mod_seq_charge as the lowest identification level
+        return "mod_seq_charge"
+
+    # For all other cases, check what's one level above leaves
+    leaf_parent_type = root_node.leaves[0].parent.type
+
+    if leaf_parent_type == "mod_seq":
+        # Scenario 2: charged peptides without fragments
+        return "base"
+    elif leaf_parent_type == "seq":
+        # Scenario 3: peptides without charge info
+        return "base"
+    elif leaf_parent_type == "gene":
+        # Scenario 4: simplest hierarchy, leaves directly under gene
+        return "base"
+    else:
+        raise ValueError(f"Unexpected tree structure: leaf parent type is '{leaf_parent_type}'. "
+                        f"Expected one of: 'mod_seq', 'seq', 'gene', or tree with 'mod_seq_charge' nodes.")
+
 def create_protnode_from_missingval_ions(gene_name,diffions, normed_c1, normed_c2):
     return MissingValProtNodeCreator(gene_name, diffions, normed_c1, normed_c2).prot_node
 
@@ -76,11 +112,22 @@ def _assign_properties_to_missingval_base_ions(self, root_node):
 
 
     @staticmethod
-    def _get_nodes_to_test(root_node): #get the nodes in the lowest level that is relevant for the binomial test
-        if root_node.leaves[0].parent.type == "mod_seq": #when AlphaQuant works with precursors only (not fragments), the precursors themselves are the "base ions" and the "mod_seq_charge" node does not exist
-            return root_node.children
-        else:
+    def _get_nodes_to_test(root_node):
+        """Get the nodes at which to perform the missing value statistical test.
+
+        Uses MISSINGVAL_TEST_LEVEL which is set once based on tree structure.
+        """
+        global MISSINGVAL_TEST_LEVEL
+
+        # Set the test level if not already determined
+        if MISSINGVAL_TEST_LEVEL is None:
+            MISSINGVAL_TEST_LEVEL = _determine_missingval_test_level(root_node)
+
+        if MISSINGVAL_TEST_LEVEL == "mod_seq_charge":
             return anytree.search.findall(root_node, filter_=lambda node: node.type == "mod_seq_charge")
+        else:  # "base"
+            # In short trees (no fragments), leaves are the precursors themselves — the right level to test
+            return root_node.leaves
 
 
     def _propagate_properties_to_nodes_to_test(self,nodes_to_test): #goes through each node to test and merges the properties from it's base to the node itself
diff --git a/alphaquant/config/quant_reader_config.yaml b/alphaquant/config/quant_reader_config.yaml
index 0b253cda..050149b6 100644
--- a/alphaquant/config/quant_reader_config.yaml
+++ b/alphaquant/config/quant_reader_config.yaml
@@ -1342,8 +1342,25 @@ 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 +1375,6 @@ fragpipe_precursors:
           - Modified Sequence
   use_iontree: False
   ml_level: SEQ
+
+
+
diff --git a/alphaquant/config/quant_reader_config_lightweight.yaml b/alphaquant/config/quant_reader_config_lightweight.yaml
deleted file mode 100644
index 74704faa..00000000
--- a/alphaquant/config/quant_reader_config_lightweight.yaml
+++ /dev/null
@@ -1,481 +0,0 @@
----
-#this file determines the parameters used to convert long format tables as e.g. produced by Spectronaut or DIA-NN into a wide table format
-alphadia_precursor_protein:
-  format: longtable
-  sample_ID: run
-  quant_ID:
-    precursor: mean_overlapping_intensity
-  protein_cols:
-   - pg_master
-  ion_hierarchy:
-    precursor:
-      order: [SEQ, MOD, CHARGE]
-      mapping:
-        SEQ:
-         - sequence
-        MOD:
-         - mods
-        CHARGE:
-         - charge
-  use_iontree: True
-  ml_level: CHARGE
-  filters:
-    protein_qval:
-      param: pg_qval
-      comparator: "<="
-      value: 0.01
-
-
-alphapept_peptides:
-  format: longtable
-  sample_ID: shortname
-  quant_ID:
-    precursor_intensity: int_sum
-  protein_cols:
-   - protein_group
-  ion_hierarchy:
-    precursor_intensity:
-      order: [SEQ, CHARGE]
-      mapping:
-        SEQ:
-         - naked_sequence
-        CHARGE:
-         - charge
-
-  use_iontree: False
-
-maxquant_peptides:
-  format: widetable
-  quant_pre_or_suffix: "Intensity "
-  protein_cols:
-   - Gene names
-  ion_cols:
-   - Sequence
-  ion_hierarchy:
-    sequence_int:
-      order: [SEQ, MOD]
-      mapping:
-        SEQ:
-          - Sequence
-        MOD:
-          - Mass
-  filters:
-    reverse:
-      param: Reverse
-      comparator: "!="
-      value: "+"
-    contaminant:
-      param: Potential contaminant
-      comparator: "!="
-      value: "+"
-    amino_acid:
-      param: Amino acid before
-      comparator: "!="
-      value: "XYZ"
-  ml_level: SEQ
-  use_iontree: False
-
-
-maxquant_evidence:
-  format: longtable
-  sample_ID: Experiment #Raw file
-  quant_ID: Intensity
-  protein_cols:
-   - Gene names
-  ion_cols:
-   - Modified sequence
-   - Charge
-
-
-diann_fragion_ms1_corrected:
-  format: longtable
-  sample_ID: Run
-  quant_ID:
-    fragion: Fragment.Quant.Corrected
-    #Fragment.Quant.Raw
-    ms1iso: Ms1.Area
-  protein_cols:
-   - Genes
-  split_cols:
-    Fragment.Quant.Corrected: ";"
-  ion_hierarchy:
-    fragion:
-      order: [SEQ, MOD, CHARGE, FRGION]
-      mapping:
-        SEQ:
-         - Stripped.Sequence
-        MOD:
-         - Modified.Sequence
-        CHARGE:
-         - Precursor.Charge
-        FRGION:
-         - Fragment.Quant.Corrected
-    ms1iso:
-      order: [SEQ, MOD, CHARGE, MS1ISOTOPES]
-      mapping:
-        SEQ:
-         - Stripped.Sequence
-        MOD:
-         - Modified.Sequence
-        CHARGE:
-         - Precursor.Charge
-        MS1ISOTOPES:
-         - Precursor.Charge
-  use_iontree: True
-  ml_level: CHARGE
-  filters:
-    protein_qval:
-      param: Lib.PG.Q.Value
-      comparator: "<="
-      value: 0.01
-
-
-diann_precursor_fragion_ms1:
-  format: longtable
-  sample_ID: Run
-  quant_ID:
-    fragion: Fragment.Quant.Raw
-    ms1iso: Ms1.Area
-    precursor: Precursor.Normalised
-  protein_cols:
-   - Genes
-  split_cols:
-    Fragment.Quant.Raw: ";"
-  ion_hierarchy:
-    fragion:
-      order: [SEQ, MOD, CHARGE, FRGION]
-      mapping:
-        SEQ:
-         - Stripped.Sequence
-        MOD:
-         - Modified.Sequence
-        CHARGE:
-         - Precursor.Charge
-        FRGION:
-         - Fragment.Quant.Raw
-    ms1iso:
-      order: [SEQ, MOD, CHARGE, MS1ISOTOPES]
-      mapping:
-        SEQ:
-         - Stripped.Sequence
-        MOD:
-         - Modified.Sequence
-        CHARGE:
-         - Precursor.Charge
-        MS1ISOTOPES:
-         - Precursor.Charge
-    precursor:
-      order: [SEQ, MOD, CHARGE, PRECURSOR]
-      mapping:
-        SEQ:
-         - Stripped.Sequence
-        MOD:
-         - Modified.Sequence
-        CHARGE:
-         - Precursor.Charge
-        PRECURSOR:
-         - Precursor.Charge
-  use_iontree: True
-  ml_level: CHARGE
-  filters:
-    protein_qval:
-      param: Lib.PG.Q.Value
-      comparator: "<="
-      value: 0.01
-
-
-diann_precursor:
-  format: longtable
-  sample_ID: Run
-  quant_ID:
-    precursor: Precursor.Normalised
-  protein_cols:
-   - Genes
-  ion_hierarchy:
-    precursor:
-      order: [SEQ, MOD, CHARGE]
-      mapping:
-        SEQ:
-         - Stripped.Sequence
-        MOD:
-         - Modified.Sequence
-        CHARGE:
-         - Precursor.Charge
-  use_iontree: True
-  ml_level: CHARGE
-  filters:
-    protein_qval:
-      param: Lib.PG.Q.Value
-      comparator: "<="
-      value: 0.01
-
-
-
-spectronaut_ptm_fragion:
-  format: longtable
-  sample_ID: R.Label
-  quant_ID:
-    fragion: F.PeakArea
-  protein_cols:
-   - ptm_id
-  ion_cols:
-   - FG.Id
-   - F.FrgIon
-   - F.FrgLossType
-   - F.Charge
-  ion_hierarchy:
-    fragion:
-      order: [SEQ, MOD, CHARGE, FRGION]
-      mapping:
-        SEQ:
-         - PEP.StrippedSequence
-        MOD:
-         - ptm_mapped_modseq
-        CHARGE:
-         - FG.Charge
-        FRGION:
-         - F.FrgIon
-         - F.FrgLossType
-         - F.Charge
-  filters:
-    fragion_intensity:
-      param: F.PeakArea
-      comparator: ">"
-      value: 5.0
-  use_iontree: True
-  ml_level: CHARGE
-  annotation_columns:
-    - PEP.StrippedSequence
-
-
-spectronaut_fragion_ms1_gene:
-  format: longtable
-  sample_ID: R.Label
-  quant_ID:
-    fragion: F.PeakArea
-    ms1iso: FG.MS1IsotopeIntensities (Measured)
-  protein_cols:
-   - PG.Genes
-  ion_cols:
-   - FG.Id
-   - F.FrgIon
-   - F.FrgLossType
-   - F.Charge
-  split_cols:
-    FG.MS1IsotopeIntensities (Measured): ";"
-  ion_hierarchy:
-    fragion:
-      order: [SEQ, MOD, CHARGE, FRGION]
-      mapping:
-        SEQ:
-         - PEP.StrippedSequence
-        MOD:
-         - EG.ModifiedSequence
-        CHARGE:
-         - FG.Charge
-        FRGION:
-         - F.FrgIon
-         - F.FrgLossType
-         - F.Charge
-    ms1iso:
-      order: [SEQ, MOD, CHARGE, MS1ISOTOPES]
-      mapping:
-        SEQ:
-         - PEP.StrippedSequence
-        MOD:
-         - EG.ModifiedSequence
-        CHARGE:
-         - FG.Charge
-        MS1ISOTOPES:
-         - FG.MS1IsotopeIntensities (Measured)
-  filters:
-    fragion_intensity:
-      param: F.PeakArea
-      comparator: ">"
-      value: 5.0
-    gene_unique:
-      param: PEP.IsGeneSpecific
-      comparator: "=="
-      value: "True"
-  use_iontree: True
-  ml_level: CHARGE
-
-
-spectronaut_fragion_ms1_gene:
-  format: longtable
-  sample_ID: R.Label
-  quant_ID:
-    fragion: F.PeakArea
-    ms1iso: FG.MS1IsotopeIntensities (Measured)
-  protein_cols:
-   - PG.Genes
-  ion_cols:
-   - FG.Id
-   - F.FrgIon
-   - F.FrgLossType
-   - F.Charge
-  split_cols:
-    FG.MS1IsotopeIntensities (Measured): ";"
-  ion_hierarchy:
-    fragion:
-      order: [SEQ, MOD, CHARGE, FRGION]
-      mapping:
-        SEQ:
-         - PEP.StrippedSequence
-        MOD:
-         - EG.ModifiedSequence
-        CHARGE:
-         - FG.Charge
-        FRGION:
-         - F.FrgIon
-         - F.FrgLossType
-         - F.Charge
-    ms1iso:
-      order: [SEQ, MOD, CHARGE, MS1ISOTOPES]
-      mapping:
-        SEQ:
-         - PEP.StrippedSequence
-        MOD:
-         - EG.ModifiedSequence
-        CHARGE:
-         - FG.Charge
-        MS1ISOTOPES:
-         - FG.MS1IsotopeIntensities (Measured)
-  filters:
-    fragion_intensity:
-      param: F.PeakArea
-      comparator: ">"
-      value: 5.0
-  use_iontree: True
-  ml_level: CHARGE
-
-
-spectronaut_precursor_gene:
-  format: longtable
-  sample_ID: R.Label
-  quant_ID:
-    precursor: FG.Quantity
-  protein_cols:
-   - PG.Genes
-  ion_hierarchy:
-    precursor:
-      order: [SEQ, MOD, CHARGE]
-      mapping:
-        SEQ:
-         - PEP.StrippedSequence
-        MOD:
-         - EG.ModifiedSequence
-        CHARGE:
-         - FG.Charge
-  filters:
-    gene_unique:
-      param: PEP.IsGeneSpecific
-      comparator: "=="
-      value: "True"
-  use_iontree: True
-  ml_level: CHARGE
-
-
-spectronaut_precursor_gene:
-  format: longtable
-  sample_ID: R.Label
-  quant_ID:
-    precursor: FG.Quantity
-  protein_cols:
-   - PG.Genes
-  ion_hierarchy:
-    precursor:
-      order: [SEQ, MOD, CHARGE]
-      mapping:
-        SEQ:
-         - PEP.StrippedSequence
-        MOD:
-         - EG.ModifiedSequence
-        CHARGE:
-         - FG.Charge
-  use_iontree: True
-  ml_level: CHARGE
-
-
-openswath_precursor_aligned:
-  format: longtable
-  sample_ID: run_id
-  quant_ID: Intensity
-  protein_cols:
-   - ProteinName
-  ion_cols:
-   - peptide_group_label
-  filters:
-    decoy:
-      param: decoy
-      comparator: "=="
-      value: 0
-
-openswath_pyprophet:
-  format: longtable
-  sample_ID: filename
-  quant_ID: Intensity
-  protein_cols:
-   - ProteinName
-  ion_cols:
-   - FullPeptideName
-   - Charge
-  filters:
-    decoy:
-      param: decoy
-      comparator: "=="
-      value: 0
-
-skyline_precursor:
-  format: longtable
-  sample_ID: ReplicateName
-  quant_ID: TotalAreaFragment
-  protein_cols:
-   - ProteinName
-  ion_cols:
-   - PeptideModifiedSequence
-   - PrecursorCharge
-
-diaumpire_precursor_ms1:
-  format: widetable
-  protein_cols:
-   - Proteins
-  ion_cols:
-   - Peptide Key
-
-
-diann_wideformat:
-  format: widetable
-  protein_cols:
-   - Protein.Group
-  ion_cols:
-   - Stripped.Sequence
-   - Modified.Sequence
-   - Precursor.Charge
-  ion_hierarchy:
-    sequence_int:
-      order: [SEQ, MOD]
-      mapping:
-        SEQ:
-          - Stripped.Sequence
-        MOD:
-          - Modified.Sequence
-        CH:
-          - Precursor.Charge
-  ml_level: SEQ
-  use_iontree: False
-
-fragpipe_precursors:
-  format: widetable
-  quant_pre_or_suffix: " Intensity"
-  protein_cols:
-   - Protein
-  ion_hierarchy:
-    sequence_int:
-      order: [SEQ, MOD]
-      mapping:
-        SEQ:
-          - Peptide Sequence
-        MOD:
-          - Modified Sequence
-  use_iontree: False