diff --git a/.gitignore b/.gitignore
index 2e47ccb6..ffd5c3e6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,11 @@
+# User defined:
+peptdeep/logs
+*.DS_Store
+*sandbox*
+*installed_models*
+*.last_checked*
+*mono_crash.*.blob
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -128,19 +136,3 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
-
-# User defined:
-peptdeep/logs
-*.DS_Store
-*sandbox*
-*installed_models*
-*.last_checked*
-
-# nbdev2
-*.gitattributes
-_docs*
-# *_quarto.yml
-# *sidebar.yml
-*_proc*
-# .gitconfig is now autogenerated
-.gitconfig
diff --git a/peptdeep/_modidx.py b/peptdeep/_modidx.py
deleted file mode 100644
index 53ce3258..00000000
--- a/peptdeep/_modidx.py
+++ /dev/null
@@ -1 +0,0 @@
-d = {"settings": {}, "syms": {}}
diff --git a/peptdeep/constants/default_settings.yaml b/peptdeep/constants/default_settings.yaml
index d01acbc2..855d993f 100644
--- a/peptdeep/constants/default_settings.yaml
+++ b/peptdeep/constants/default_settings.yaml
@@ -265,10 +265,9 @@ library:
   max_precursor_mz: 2000.0
   decoy: None
   decoy_choices:
-  - protein_reverse
+  - None
   - pseudo_reverse
   - diann
-  - None
   max_frag_charge: 2
   frag_types:
   - b
diff --git a/peptdeep/webui/rescore_ui.py b/peptdeep/webui/rescore_ui.py
index f586d885..d2122e40 100644
--- a/peptdeep/webui/rescore_ui.py
+++ b/peptdeep/webui/rescore_ui.py
@@ -1,7 +1,5 @@
 import streamlit as st
-import pandas as pd
 import os
-import time
 
 from .ui_utils import files_in_folder_pandas
 from peptdeep.settings import global_settings
diff --git a/peptdeep/webui/server.py b/peptdeep/webui/server.py
index fae9d42b..601aa8cb 100644
--- a/peptdeep/webui/server.py
+++ b/peptdeep/webui/server.py
@@ -1,6 +1,5 @@
 import time
 import os
-import sys
 import shutil
 import multiprocessing as mp
 
diff --git a/peptdeep/webui/server_ui.py b/peptdeep/webui/server_ui.py
index d27d79e3..5d36c9f2 100644
--- a/peptdeep/webui/server_ui.py
+++ b/peptdeep/webui/server_ui.py
@@ -1,7 +1,6 @@
 import streamlit as st
 import os
 import psutil
-import time
 
 from alphabase.yaml_utils import load_yaml
 
diff --git a/peptdeep/webui/settings_ui.py b/peptdeep/webui/settings_ui.py
index a2069ee3..7c1d0925 100644
--- a/peptdeep/webui/settings_ui.py
+++ b/peptdeep/webui/settings_ui.py
@@ -9,10 +9,9 @@
 from peptdeep.settings import (
     update_settings,
     add_user_defined_modifications,
+    global_settings,
 )
 
-from peptdeep.settings import global_settings
-
 global_ui_settings = global_settings
 
 
diff --git a/peptdeep/webui/transfer_ui.py b/peptdeep/webui/transfer_ui.py
index 8414cafe..30e73db3 100644
--- a/peptdeep/webui/transfer_ui.py
+++ b/peptdeep/webui/transfer_ui.py
@@ -1,12 +1,10 @@
 import streamlit as st
 import pandas as pd
 import os
-import time
 from datetime import datetime
 
 from alphabase.yaml_utils import save_yaml
 from alphabase.constants.modification import MOD_DF
-import alphabase.psm_reader
 
 from peptdeep.webui.server import queue_folder
 from peptdeep.webui.ui_utils import (
@@ -147,6 +145,7 @@ def show():
         "maxquant": "msms.txt",
         "diann": "tsv",
         "speclib_tsv": "tsv",
+        "msfragger_pepxml": "pepxml",
     }
     used_psm_types = list(psm_type_to_ext_dict.keys())