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@@ -1176,14 +992,14 @@
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@@ -1315,7 +1131,7 @@
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@@ -1337,8 +1153,8 @@
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diff --git a/docs/images/formats-relation.svg b/docs/images/formats-relation.svg
index 817a802..7ef291d 100644
Binary files a/docs/images/formats-relation.svg and b/docs/images/formats-relation.svg differ
diff --git a/quantmsio/core/common.py b/quantmsio/core/common.py
index 8484aaa..215253c 100644
--- a/quantmsio/core/common.py
+++ b/quantmsio/core/common.py
@@ -64,7 +64,7 @@
     "Stripped.Sequence": "sequence",
     "Modified.Sequence": "peptidoform",
     "Genes": "gg_names",
-    "Run": "run"
+    "Run": "run",
 }
 DIANN_USECOLS = list(DIANN_MAP.keys())
 
diff --git a/quantmsio/core/diann.py b/quantmsio/core/diann.py
index 233b3a4..8e332ef 100644
--- a/quantmsio/core/diann.py
+++ b/quantmsio/core/diann.py
@@ -17,7 +17,9 @@
 from quantmsio.utils.pride_utils import generate_scan_number
 from quantmsio.core.common import DIANN_MAP, DIANN_USECOLS
 
-DIANN_SQL = ', '.join([f'"{name}"' for name in DIANN_USECOLS])
+DIANN_SQL = ", ".join([f'"{name}"' for name in DIANN_USECOLS])
+
+
 class DiaNNConvert(DuckDB):
 
     def __init__(self, diann_report, sdrf_path, duckdb_max_memory="16GB", duckdb_threads=4):
@@ -46,8 +48,7 @@ def get_report_from_database(self, runs: list) -> pd.DataFrame:
             from report
             where Run IN {}
             """.format(
-                DIANN_SQL,
-                tuple(runs)
+                DIANN_SQL, tuple(runs)
             )
         )
         report = database.df()
@@ -190,7 +191,7 @@ def add_additional_msg(self, report: pd.DataFrame):
                     "channel": rows["channel"],
                     "additional_intensity": [
                         {"intensity_name": "normalize_intensity", "intensity_value": rows["normalize_intensity"]},
-                        {"intensity_name": "lfq", "intensity_value": rows["lfq"]}
+                        {"intensity_name": "lfq", "intensity_value": rows["lfq"]},
                     ],
                 }
             ],
@@ -200,7 +201,7 @@ def add_additional_msg(self, report: pd.DataFrame):
             lambda row: [
                 {"score_name": "qvalue", "score_value": row["qvalue"]},
                 {"score_name": "pg_qvalue", "score_value": row["pg_qvalue"]},
-                {"score_name": "global_qvalue", "score_value": row["global_qvalue"]}
+                {"score_name": "global_qvalue", "score_value": row["global_qvalue"]},
             ],
             axis=1,
         )
@@ -208,7 +209,7 @@ def add_additional_msg(self, report: pd.DataFrame):
             lambda rows: [
                 {"cv_name": "precursor_quantification_score", "cv_value": str(rows["precursor_quantification_score"])}
             ],
-            axis=1
+            axis=1,
         )
         report.loc[:, "scan_reference_file_name"] = None
         report.loc[:, "gg_accessions"] = None
diff --git a/quantmsio/core/mztab.py b/quantmsio/core/mztab.py
index 0e47d62..0a3d1db 100644
--- a/quantmsio/core/mztab.py
+++ b/quantmsio/core/mztab.py
@@ -244,8 +244,8 @@ def get_mods_map(self):
                     accession = values[1].strip()
                     name = values[2].strip()
                     line = f.readline()
-                    site = line.replace("\n","").split("\t")[2]
-                    mods_map[name] = [accession.upper(),site]
+                    site = line.replace("\n", "").split("\t")[2]
+                    mods_map[name] = [accession.upper(), site]
                     mods_map[accession.upper().upper()] = [name, site]
             line = f.readline()
         f.close()
diff --git a/quantmsio/core/psm.py b/quantmsio/core/psm.py
index 673a1e4..5f6f98d 100644
--- a/quantmsio/core/psm.py
+++ b/quantmsio/core/psm.py
@@ -78,7 +78,9 @@ def extract_from_pep(self, chunksize=2000000):
             pep.reset_index(drop=True, inplace=True)
             if "opt_global_cv_MS:1000889_peptidoform_sequence" not in pep.columns:
                 pep.loc[:, "opt_global_cv_MS:1000889_peptidoform_sequence"] = pep[["modifications", "sequence"]].apply(
-                    lambda row: get_petidoform_msstats_notation(row["sequence"], row["modifications"], self._modifications),
+                    lambda row: get_petidoform_msstats_notation(
+                        row["sequence"], row["modifications"], self._modifications
+                    ),
                     axis=1,
                 )
             # check spectra_ref
@@ -108,9 +110,9 @@ def extract_from_pep(self, chunksize=2000000):
                 if key not in pep_map:
                     pep_map[key] = value
                 elif value[0] < pep_map[key][0]:
-                        pep_map[key] = value
+                    pep_map[key] = value
         return pep_map
-    
+
     @staticmethod
     def slice(df, partitions):
         cols = df.columns