diff --git a/proteobench/io/parsing/io_parse_settings/parse_settings_alphadia.toml b/proteobench/io/parsing/io_parse_settings/parse_settings_alphadia.toml
index 4a30703b..c3feaf49 100644
--- a/proteobench/io/parsing/io_parse_settings/parse_settings_alphadia.toml
+++ b/proteobench/io/parsing/io_parse_settings/parse_settings_alphadia.toml
@@ -3,6 +3,7 @@
 "run" = "Raw file"
 "charge" = "Charge"
 "intensity" = "Intensity"
+"genes" = "Proteins" 
 
 [condition_mapper]
 "LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01" = "A"
diff --git a/proteobench/io/parsing/io_parse_settings/parse_settings_fragpipe_DIA.toml b/proteobench/io/parsing/io_parse_settings/parse_settings_fragpipe_DIA.toml
index 2e3e5604..ee03d89e 100644
--- a/proteobench/io/parsing/io_parse_settings/parse_settings_fragpipe_DIA.toml
+++ b/proteobench/io/parsing/io_parse_settings/parse_settings_fragpipe_DIA.toml
@@ -29,8 +29,8 @@
 "before_aa" = false
 "isalpha" = true
 "isupper" = true
-"pattern"="\\[([^]]+)\\]"
-"modification_dict" = {"[57.0215]" = "Carbamidomethyl", "[57.0216]" = "Carbamidomethyl", "[15.9949]" = "Oxidation", "[-17.026548]" = "Gln->pyro-Glu", "[-18.010565]" = "Glu->pyro-Glu", "[42.0106]" = "Acetyl"}
+"pattern"="(?<=\\[).+?(?=\\])"
+"modification_dict" = {"57.0215" = "Carbamidomethyl", "57.0216" = "Carbamidomethyl", "15.9949" = "Oxidation", "-17.026548" = "Gln->pyro-Glu", "-18.010565" = "Glu->pyro-Glu", "42.0106" = "Acetyl"}
 
 [general]
 "contaminant_flag" = "Cont_"
diff --git a/proteobench/io/parsing/io_parse_settings/parse_settings_spectronaut.toml b/proteobench/io/parsing/io_parse_settings/parse_settings_spectronaut.toml
index 47bcdb5c..ffdc0cae 100644
--- a/proteobench/io/parsing/io_parse_settings/parse_settings_spectronaut.toml
+++ b/proteobench/io/parsing/io_parse_settings/parse_settings_spectronaut.toml
@@ -3,6 +3,7 @@
 "R.FileName" = "Raw file"
 "FG.Charge" = "Charge"
 "FG.Quantity" = "Intensity"
+"PG.ProteinGroups" = "Proteins"
 
 [condition_mapper]
 "LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01" = "A"
diff --git a/proteobench/io/parsing/parse_ion.py b/proteobench/io/parsing/parse_ion.py
index 80dfcabd..917e26a8 100644
--- a/proteobench/io/parsing/parse_ion.py
+++ b/proteobench/io/parsing/parse_ion.py
@@ -50,7 +50,7 @@ def load_input_file(input_csv: str, input_format: str) -> pd.DataFrame:
         mapper_path = os.path.join(os.path.dirname(__file__), "io_parse_settings/mapper.csv")
         mapper_df = pd.read_csv(mapper_path).set_index("gene_name")
         mapper = mapper_df["description"].to_dict()
-        input_data_frame["Proteins"] = input_data_frame["genes"].map(
+        input_data_frame["genes"] = input_data_frame["genes"].map(
             lambda x: ";".join([mapper[protein] if protein in mapper.keys() else protein for protein in x.split(";")])
         )
         input_data_frame["proforma"] = input_data_frame.apply(
@@ -75,11 +75,11 @@ def load_input_file(input_csv: str, input_format: str) -> pd.DataFrame:
         mapper_path = os.path.join(os.path.dirname(__file__), "io_parse_settings/mapper.csv")
         mapper_df = pd.read_csv(mapper_path).set_index("gene_name")
         mapper = mapper_df["description"].to_dict()
-        input_data_frame["Protein_list"] = input_data_frame["PG.ProteinGroups"].str.split(";")
-        input_data_frame["Proteins"] = input_data_frame["Protein_list"].map(
+        input_data_frame["PG.ProteinGroups"] = input_data_frame["PG.ProteinGroups"].str.split(";")
+        input_data_frame["PG.ProteinGroups"] = input_data_frame["PG.ProteinGroups"].map(
             lambda x: [mapper[protein] if protein in mapper.keys() else protein for protein in x]
         )
-        input_data_frame["Proteins"] = input_data_frame["Proteins"].str.join(";")
+        input_data_frame["PG.ProteinGroups"] = input_data_frame["PG.ProteinGroups"].str.join(";")
     elif input_format == "MSAID":
         input_data_frame = pd.read_csv(input_csv, low_memory=False, sep="\t")