diff --git a/.gitignore b/.gitignore
index 57623e22..8eaababa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,9 @@ old_files/
 prepare_pin_files.py
 *.jar
 
+# Ruff
+.ruff_cache/
+
 # Atom remote-sync config
 .remote-sync.json
 
@@ -90,6 +93,7 @@ celerybeat-schedule
 # virtualenv
 venv/
 ENV/
+.venv*/
 
 # Spyder project settings
 .spyderproject
@@ -99,5 +103,4 @@ ENV/
 
 # vscode
 .vscode/
-.pytest_cache/v/cache/nodeids
-.pytest_cache/v/cache/stepwise
+.pytest_cache/
diff --git a/docs/source/userguide/configuration.rst b/docs/source/userguide/configuration.rst
index 081a9b68..a857bf43 100644
--- a/docs/source/userguide/configuration.rst
+++ b/docs/source/userguide/configuration.rst
@@ -26,8 +26,9 @@ denotes the official Unimod name.
 
 To correctly parse the various notations to ProForma, :py:mod:`psm_utils.io` readers
 require :py:obj:`modification_definitions` that map each specific search engine
-modification label to a valid ProForma label. :py:obj:`modification_definitions` is defined as a :py:obj:`list` of :py:obj:`dict`'s.
-Each :py:obj:`dict` should contain the following key-value pairs:
+modification label to a valid ProForma label. :py:obj:`modification_definitions` is defined as a
+:py:obj:`list` of :py:obj:`dict`'s. Each :py:obj:`dict` should contain the following key-value
+pairs:
 
     - ``site``: Amino acids or peptide termini where the modification occurs. Should be
       the IUPAC one-letter code for amino acid residues and `N-term` or `C-term` for
diff --git a/examples/readme.txt b/examples/readme.txt
index bafaebbb..59c391af 100644
--- a/examples/readme.txt
+++ b/examples/readme.txt
@@ -4,6 +4,6 @@ Raw file converted to MGF with the Compomics ThermoRawFileParser (https://github
 
 Searched with MaxQuant v1.6.2.3 with all parameters as described in the dataset's original article, with FDR-filtering set to 1 (no filtering)
 Also searched with MS-GF+ v2019.02.28
-MS²ReScore tested with Percolator version 3.02.1
+MS²Rescore tested with Percolator version 3.02.1
 
 Fasta file downloaded from https://www.uniprot.org/proteomes/UP000005640 and https://www.thegpm.org/crap/
diff --git a/ms2rescore/__main__.py b/ms2rescore/__main__.py
index 33ddb6df..46d29ce0 100644
--- a/ms2rescore/__main__.py
+++ b/ms2rescore/__main__.py
@@ -32,8 +32,8 @@
 CONSOLE = Console(record=True)
 
 
-def _build_credits():
-    """Build credits."""
+def _print_credits():
+    """Print software credits to terminal."""
     text = Text()
     text.append("\n")
     text.append("MS²Rescore", style="bold link https://github.com/compomics/ms2rescore")
@@ -45,8 +45,7 @@ def _build_credits():
     )
     text.append("\n")
     text.stylize("cyan")
-    return text
-
+    CONSOLE.print(text)
 
 def _setup_logging(passed_level: str, log_file: Union[str, Path]):
     """Setup logging for writing to log file and Rich Console."""
@@ -146,7 +145,7 @@ def _parse_arguments() -> argparse.Namespace:
 
 def main():
     """Run MS²Rescore command-line interface."""
-    CONSOLE.print(_build_credits())
+    _print_credits()
 
     cli_args = _parse_arguments()
     if cli_args.config_file:
@@ -154,10 +153,15 @@ def main():
     else:
         config = parse_configurations(cli_args)
 
-    output_file_root = Path(config["ms2rescore"]["psm_file"]).with_suffix("")
-    _setup_logging(
-        config["ms2rescore"]["log_level"], str(output_file_root) + "-ms2rescore-log.txt"
-    )
+    if config["ms2rescore"]["output_path"]:
+        output_file_root = (
+            Path(config["ms2rescore"]["output_path"])
+            / Path(config["ms2rescore"]["psm_file"]).stem
+        ).as_posix()
+    else:
+        output_file_root = Path(config["ms2rescore"]["psm_file"]).with_suffix("").as_posix()
+
+    _setup_logging(config["ms2rescore"]["log_level"], output_file_root + "-ms2rescore-log.txt")
 
     try:
         ms2rescore = MS2Rescore(configuration=config)
diff --git a/ms2rescore/feature_generators/ms2pip.py b/ms2rescore/feature_generators/ms2pip.py
index 2f1ee6ad..613ebf79 100644
--- a/ms2rescore/feature_generators/ms2pip.py
+++ b/ms2rescore/feature_generators/ms2pip.py
@@ -5,7 +5,6 @@
 import warnings
 from itertools import chain
 from typing import List, Optional, Union
-import math
 
 import numpy as np
 import pandas as pd
@@ -304,7 +303,7 @@ def _calculate_features_single(self, processing_result: ProcessingResult) -> Uni
         features = dict(
             zip(
                 self.feature_names,
-                [0.0 if math.isnan(ft) else ft for ft in feature_values],
+                [0.0 if np.isnan(ft) else ft for ft in feature_values],
             )
         )
 
diff --git a/ms2rescore/gui/app.py b/ms2rescore/gui/app.py
index 45b8b518..8cae445d 100644
--- a/ms2rescore/gui/app.py
+++ b/ms2rescore/gui/app.py
@@ -356,7 +356,7 @@ def __init__(self, *args, **kwargs):
         self.configure(fg_color="transparent")
         self.grid_columnconfigure(0, weight=1)
 
-        self.title = ctk.CTkLabel(self, text="MS²PIP", fg_color="gray30", corner_radius=6)
+        self.title = widgets.Heading(self, text="MS²PIP")
         self.title.grid(row=0, column=0, columnspan=2, pady=(0, 5), sticky="ew")
 
         self.enabled = widgets.LabeledSwitch(self, label="Enable MS²PIP", default=True)
@@ -393,7 +393,7 @@ def __init__(self, *args, **kwargs):
         self.configure(fg_color="transparent")
         self.grid_columnconfigure(0, weight=1)
 
-        self.title = ctk.CTkLabel(self, text="DeepLC", fg_color="gray30", corner_radius=6)
+        self.title = widgets.Heading(self, text="DeepLC")
         self.title.grid(row=0, column=0, columnspan=2, pady=(0, 5), sticky="ew")
 
         self.enabled = widgets.LabeledSwitch(self, label="Enable DeepLC", default=True)
@@ -461,6 +461,7 @@ def function(config):
 
 
 def app():
+    """Start the application."""
     root = Function2CTk(
         sidebar_frame=SideBar,
         config_frame=ConfigFrame,
diff --git a/ms2rescore/gui/function2ctk.py b/ms2rescore/gui/function2ctk.py
index a1616124..eb43902f 100644
--- a/ms2rescore/gui/function2ctk.py
+++ b/ms2rescore/gui/function2ctk.py
@@ -230,10 +230,10 @@ def __init__(
         self.stop_callback = stop_callback
         self.stop_button_pressed = False
 
-        self.grid_columnconfigure(0, weight=2)
-        self.grid_columnconfigure(1, weight=1)
+        self.grid_columnconfigure(0, weight=1)
+        self.grid_columnconfigure(1, minsize=140)
 
-        self.progress_bar = ctk.CTkProgressBar(self)  # , width=150)
+        self.progress_bar = ctk.CTkProgressBar(self)
 
         self.start_button = ctk.CTkButton(master=self, command=self._start_callback, text="Start")
         self.stop_button = ctk.CTkButton(master=self, command=self._stop_callback, text="Stop")
@@ -259,7 +259,7 @@ def _start_callback(self):
         self.stop_button.grid(row=0, column=1, sticky="ew")
 
         # Show and activate progress bar
-        self.progress_bar.grid(row=0, column=0, sticky="ew")
+        self.progress_bar.grid(row=0, column=0, sticky="ew", padx=10)
         self.progress_bar.configure(mode="indeterminate")
         self.progress_bar.start()
 
diff --git a/ms2rescore/gui/widgets.py b/ms2rescore/gui/widgets.py
index fc2618fc..d4b4a4f6 100644
--- a/ms2rescore/gui/widgets.py
+++ b/ms2rescore/gui/widgets.py
@@ -7,6 +7,16 @@
 import customtkinter as ctk
 
 
+class Heading(ctk.CTkLabel):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.configure(
+            fg_color=("gray80", "gray30"),
+            text_color=("black", "white"),
+            corner_radius=6,
+        )
+
+
 class LabeledEntry(ctk.CTkFrame):
     def __init__(self, *args, label="Enter text", placeholder_text="Enter text...", **kwargs):
         super().__init__(*args, **kwargs)
@@ -58,10 +68,8 @@ def __init__(self, *args, label="Select option", options=[], default_value=None,
 
         self._radio_buttons = []
         for i, option in enumerate(options):
-            radio_button = ctk.CTkRadioButton(
-                self, text=option, variable=self.value, value=option
-            )
-            radio_button.grid(row=i+1, column=0, padx=0, pady=(0, 5), sticky="w")
+            radio_button = ctk.CTkRadioButton(self, text=option, variable=self.value, value=option)
+            radio_button.grid(row=i + 1, column=0, padx=0, pady=(0, 5), sticky="w")
             self._radio_buttons.append(radio_button)
 
     def get(self):
@@ -316,7 +324,13 @@ def __init__(self, *args, label=None, columns=2, header_labels=["A", "B"], **kwa
         for i, header in enumerate(self.header_labels):
             header_row.grid_columnconfigure(i, weight=1, uniform=self.uniform_hash)
             padx = (0, 5) if i < len(self.header_labels) - 1 else (0, 0)
-            label = ctk.CTkLabel(header_row, text=header, fg_color="gray30", corner_radius=6)
+            label = ctk.CTkLabel(
+                header_row,
+                text=header,
+                fg_color=("gray80", "gray30"),
+                text_color=("black", "white"),
+                corner_radius=6,
+            )
             label.grid(row=0, column=i, padx=padx, sticky="ew")
 
         # Input rows
diff --git a/ms2rescore/ms2rescore_main.py b/ms2rescore/ms2rescore_main.py
index 140ee309..c81078bb 100644
--- a/ms2rescore/ms2rescore_main.py
+++ b/ms2rescore/ms2rescore_main.py
@@ -10,7 +10,7 @@
 
 from ms2rescore.exceptions import MS2RescoreConfigurationError, MS2RescoreError
 from ms2rescore.feature_generators import FEATURE_GENERATORS
-from ms2rescore.rescoring_engines import percolator
+from ms2rescore.rescoring_engines import mokapot, percolator
 
 logger = logging.getLogger(__name__)
 
@@ -86,6 +86,11 @@ def run(self):
         # Ensure that spectrum IDs are strings (Pydantic 2.0 does not coerce int to str)
         psm_list["spectrum_id"] = [str(spec_id) for spec_id in psm_list["spectrum_id"]]
 
+        # Store values for comparison later
+        psm_data_before = psm_list.to_dataframe()[
+            ["score", "qvalue", "pep", "is_decoy", "rank"]
+        ].copy()
+
         # Add rescoring features
         feature_names = dict()
         for fgen_name, fgen_config in self.config["feature_generators"].items():
@@ -114,6 +119,7 @@ def run(self):
             logging.debug(f"Creating USIs for {len(psm_list)} PSMs")
             psm_list["spectrum_id"] = [psm.get_usi(as_url=False) for psm in psm_list]
 
+        # Rescore PSMs
         if "percolator" in self.config["rescoring_engine"]:
             percolator.rescore(
                 psm_list,
@@ -124,7 +130,31 @@ def run(self):
             )
 
         elif "mokapot" in self.config["rescoring_engine"]:
-            raise NotImplementedError()
+            mokapot.rescore(psm_list, mokapot_kwargs=self.config["rescoring_engine"]["mokapot"])
+
+        psm_data_after = psm_list.to_dataframe()[
+            ["score", "qvalue", "pep", "is_decoy", "rank"]
+        ].copy()
+
+        # Compare results
+        id_psms_before = (
+            (psm_data_before["qvalue"] < 0.01) & (psm_data_before["is_decoy"] == False)
+        ).sum()
+        id_psms_after = (
+            (psm_data_after["qvalue"] < 0.01) & (psm_data_after["is_decoy"] == False)
+        ).sum()
+        diff = id_psms_after - id_psms_before
+        diff_perc = diff / id_psms_before
+        logger.info(f"Identified {diff} ({diff_perc:.2%}) more PSMs at 1% FDR after rescoring.")
+
+        # Write output
+        logger.info(f"Writing output to {self.output_file_root}.psms.tsv...")
+        psm_utils.io.write_file(
+            psm_list,
+            self.output_file_root + ".psms.tsv",
+            filetype="tsv",
+            show_progressbar=True,
+        )
 
 
 def _match_psm_ids(old_id, regex_pattern):
diff --git a/ms2rescore/package_data/ms2rescore-gui-theme.json b/ms2rescore/package_data/ms2rescore-gui-theme.json
index f78766c2..92c89cf1 100644
--- a/ms2rescore/package_data/ms2rescore-gui-theme.json
+++ b/ms2rescore/package_data/ms2rescore-gui-theme.json
@@ -1,155 +1,155 @@
 {
-  "CTk": {
-    "fg_color": ["gray95", "gray10"]
-  },
-  "CTkToplevel": {
-    "fg_color": ["gray95", "gray10"]
-  },
-  "CTkFrame": {
-    "corner_radius": 6,
-    "border_width": 0,
-    "fg_color": ["gray90", "gray13"],
-    "top_fg_color": ["gray85", "gray16"],
-    "border_color": ["gray65", "gray28"]
-  },
-  "CTkButton": {
-    "corner_radius": 6,
-    "border_width": 0,
-    "fg_color": ["#3a7ebf", "#1f538d"],
-    "hover_color": ["#325882", "#14375e"],
-    "border_color": ["#3E454A", "#949A9F"],
-    "text_color": ["#DCE4EE", "#DCE4EE"],
-    "text_color_disabled": ["gray74", "gray60"]
-  },
-  "CTkLabel": {
-    "corner_radius": 0,
-    "fg_color": "transparent",
-    "text_color": ["gray14", "gray84"]
-  },
-  "CTkEntry": {
-    "corner_radius": 6,
-    "border_width": 2,
-    "fg_color": ["#F9F9FA", "#343638"],
-    "border_color": ["#979DA2", "#565B5E"],
-    "text_color": ["gray14", "gray84"],
-    "placeholder_text_color": ["gray52", "gray62"]
-  },
-  "CTkCheckbox": {
-    "corner_radius": 6,
-    "border_width": 3,
-    "fg_color": ["#3a7ebf", "#1f538d"],
-    "border_color": ["#3E454A", "#949A9F"],
-    "hover_color": ["#325882", "#14375e"],
-    "checkmark_color": ["#DCE4EE", "gray90"],
-    "text_color": ["gray14", "gray84"],
-    "text_color_disabled": ["gray60", "gray45"]
-  },
-  "CTkSwitch": {
-    "corner_radius": 1000,
-    "border_width": 3,
-    "button_length": 0,
-    "fg_color": ["#939BA2", "#4A4D50"],
-    "progress_color": ["#3a7ebf", "#1f538d"],
-    "button_color": ["gray36", "#D5D9DE"],
-    "button_hover_color": ["gray20", "gray100"],
-    "text_color": ["gray14", "gray84"],
-    "text_color_disabled": ["gray60", "gray45"]
-  },
-  "CTkRadiobutton": {
-    "corner_radius": 1000,
-    "border_width_checked": 6,
-    "border_width_unchecked": 3,
-    "fg_color": ["#3a7ebf", "#1f538d"],
-    "border_color": ["#3E454A", "#949A9F"],
-    "hover_color": ["#325882", "#14375e"],
-    "text_color": ["gray14", "gray84"],
-    "text_color_disabled": ["gray60", "gray45"]
-  },
-  "CTkProgressBar": {
-    "corner_radius": 1000,
-    "border_width": 0,
-    "fg_color": ["#939BA2", "#4A4D50"],
-    "progress_color": ["#3a7ebf", "#1f538d"],
-    "border_color": ["gray", "gray"]
-  },
-  "CTkSlider": {
-    "corner_radius": 1000,
-    "button_corner_radius": 1000,
-    "border_width": 6,
-    "button_length": 0,
-    "fg_color": ["#939BA2", "#4A4D50"],
-    "progress_color": ["gray40", "#AAB0B5"],
-    "button_color": ["#3a7ebf", "#1f538d"],
-    "button_hover_color": ["#325882", "#14375e"]
-  },
-  "CTkOptionMenu": {
-    "corner_radius": 6,
-    "fg_color": ["#3a7ebf", "#1f538d"],
-    "button_color": ["#325882", "#14375e"],
-    "button_hover_color": ["#234567", "#1e2c40"],
-    "text_color": ["#DCE4EE", "#DCE4EE"],
-    "text_color_disabled": ["gray74", "gray60"]
-  },
-  "CTkComboBox": {
-    "corner_radius": 6,
-    "border_width": 2,
-    "fg_color": ["#F9F9FA", "#343638"],
-    "border_color": ["#979DA2", "#565B5E"],
-    "button_color": ["#979DA2", "#565B5E"],
-    "button_hover_color": ["#6E7174", "#7A848D"],
-    "text_color": ["gray14", "gray84"],
-    "text_color_disabled": ["gray50", "gray45"]
-  },
-  "CTkScrollbar": {
-    "corner_radius": 1000,
-    "border_spacing": 4,
-    "fg_color": "transparent",
-    "button_color": ["gray55", "gray41"],
-    "button_hover_color": ["gray40", "gray53"]
-  },
-  "CTkSegmentedButton": {
-    "corner_radius": 6,
-    "border_width": 2,
-    "fg_color": ["#979DA2", "gray29"],
-    "selected_color": ["#3a7ebf", "#1f538d"],
-    "selected_hover_color": ["#325882", "#14375e"],
-    "unselected_color": ["#979DA2", "gray29"],
-    "unselected_hover_color": ["gray70", "gray41"],
-    "text_color": ["#DCE4EE", "#DCE4EE"],
-    "text_color_disabled": ["gray74", "gray60"]
-  },
-  "CTkTextbox": {
-    "corner_radius": 6,
-    "border_width": 0,
-    "fg_color": ["gray100", "gray20"],
-    "border_color": ["#979DA2", "#565B5E"],
-    "text_color": ["gray14", "gray84"],
-    "scrollbar_button_color": ["gray55", "gray41"],
-    "scrollbar_button_hover_color": ["gray40", "gray53"]
-  },
-  "CTkScrollableFrame": {
-    "label_fg_color": ["gray80", "gray21"]
-  },
-  "DropdownMenu": {
-    "fg_color": ["gray90", "gray20"],
-    "hover_color": ["gray75", "gray28"],
-    "text_color": ["gray14", "gray84"]
-  },
-  "CTkFont": {
-    "macOS": {
-      "family": "SF Display",
-      "size": 13,
-      "weight": "normal"
-    },
-    "Windows": {
-      "family": "Roboto",
-      "size": 13,
-      "weight": "normal"
-    },
-    "Linux": {
-      "family": "Roboto",
-      "size": 13,
-      "weight": "normal"
+    "CTk": {
+        "fg_color": ["gray95", "gray10"]
+    },
+    "CTkToplevel": {
+        "fg_color": ["gray95", "gray10"]
+    },
+    "CTkFrame": {
+        "corner_radius": 6,
+        "border_width": 0,
+        "fg_color": ["gray90", "gray13"],
+        "top_fg_color": ["gray85", "gray16"],
+        "border_color": ["gray65", "gray28"]
+    },
+    "CTkButton": {
+        "corner_radius": 6,
+        "border_width": 0,
+        "fg_color": ["#3a7ebf", "#1f538d"],
+        "hover_color": ["#325882", "#14375e"],
+        "border_color": ["#3E454A", "#949A9F"],
+        "text_color": ["#DCE4EE", "#DCE4EE"],
+        "text_color_disabled": ["gray74", "gray60"]
+    },
+    "CTkLabel": {
+        "corner_radius": 0,
+        "fg_color": "transparent",
+        "text_color": ["gray14", "gray84"]
+    },
+    "CTkEntry": {
+        "corner_radius": 6,
+        "border_width": 2,
+        "fg_color": ["#F9F9FA", "#343638"],
+        "border_color": ["#979DA2", "#565B5E"],
+        "text_color": ["gray14", "gray84"],
+        "placeholder_text_color": ["gray52", "gray62"]
+    },
+    "CTkCheckbox": {
+        "corner_radius": 6,
+        "border_width": 3,
+        "fg_color": ["#3a7ebf", "#1f538d"],
+        "border_color": ["#3E454A", "#949A9F"],
+        "hover_color": ["#325882", "#14375e"],
+        "checkmark_color": ["#DCE4EE", "gray90"],
+        "text_color": ["gray14", "gray84"],
+        "text_color_disabled": ["gray60", "gray45"]
+    },
+    "CTkSwitch": {
+        "corner_radius": 1000,
+        "border_width": 3,
+        "button_length": 0,
+        "fg_color": ["#939BA2", "#4A4D50"],
+        "progress_color": ["#3a7ebf", "#1f538d"],
+        "button_color": ["gray36", "#D5D9DE"],
+        "button_hover_color": ["gray20", "gray100"],
+        "text_color": ["gray14", "gray84"],
+        "text_color_disabled": ["gray60", "gray45"]
+    },
+    "CTkRadiobutton": {
+        "corner_radius": 1000,
+        "border_width_checked": 6,
+        "border_width_unchecked": 3,
+        "fg_color": ["#3a7ebf", "#1f538d"],
+        "border_color": ["#3E454A", "#949A9F"],
+        "hover_color": ["#325882", "#14375e"],
+        "text_color": ["gray14", "gray84"],
+        "text_color_disabled": ["gray60", "gray45"]
+    },
+    "CTkProgressBar": {
+        "corner_radius": 1000,
+        "border_width": 0,
+        "fg_color": ["#939BA2", "#4A4D50"],
+        "progress_color": ["#3a7ebf", "#1f538d"],
+        "border_color": ["gray", "gray"]
+    },
+    "CTkSlider": {
+        "corner_radius": 1000,
+        "button_corner_radius": 1000,
+        "border_width": 6,
+        "button_length": 0,
+        "fg_color": ["#939BA2", "#4A4D50"],
+        "progress_color": ["gray40", "#AAB0B5"],
+        "button_color": ["#3a7ebf", "#1f538d"],
+        "button_hover_color": ["#325882", "#14375e"]
+    },
+    "CTkOptionMenu": {
+        "corner_radius": 6,
+        "fg_color": ["#3a7ebf", "#1f538d"],
+        "button_color": ["#325882", "#14375e"],
+        "button_hover_color": ["#234567", "#1e2c40"],
+        "text_color": ["#DCE4EE", "#DCE4EE"],
+        "text_color_disabled": ["gray74", "gray60"]
+    },
+    "CTkComboBox": {
+        "corner_radius": 6,
+        "border_width": 2,
+        "fg_color": ["#F9F9FA", "#343638"],
+        "border_color": ["#979DA2", "#565B5E"],
+        "button_color": ["#979DA2", "#565B5E"],
+        "button_hover_color": ["#6E7174", "#7A848D"],
+        "text_color": ["gray14", "gray84"],
+        "text_color_disabled": ["gray50", "gray45"]
+    },
+    "CTkScrollbar": {
+        "corner_radius": 1000,
+        "border_spacing": 4,
+        "fg_color": "transparent",
+        "button_color": ["gray55", "gray41"],
+        "button_hover_color": ["gray40", "gray53"]
+    },
+    "CTkSegmentedButton": {
+        "corner_radius": 6,
+        "border_width": 2,
+        "fg_color": ["#979DA2", "gray29"],
+        "selected_color": ["#3a7ebf", "#1f538d"],
+        "selected_hover_color": ["#325882", "#14375e"],
+        "unselected_color": ["#979DA2", "gray29"],
+        "unselected_hover_color": ["gray70", "gray41"],
+        "text_color": ["#DCE4EE", "#DCE4EE"],
+        "text_color_disabled": ["gray74", "gray60"]
+    },
+    "CTkTextbox": {
+        "corner_radius": 6,
+        "border_width": 0,
+        "fg_color": ["gray100", "gray20"],
+        "border_color": ["#979DA2", "#565B5E"],
+        "text_color": ["gray14", "gray84"],
+        "scrollbar_button_color": ["gray55", "gray41"],
+        "scrollbar_button_hover_color": ["gray40", "gray53"]
+    },
+    "CTkScrollableFrame": {
+        "label_fg_color": ["gray80", "gray21"]
+    },
+    "DropdownMenu": {
+        "fg_color": ["gray90", "gray20"],
+        "hover_color": ["gray75", "gray28"],
+        "text_color": ["gray14", "gray84"]
+    },
+    "CTkFont": {
+        "macOS": {
+            "family": "SF Display",
+            "size": 13,
+            "weight": "normal"
+        },
+        "Windows": {
+            "family": "Roboto",
+            "size": 13,
+            "weight": "normal"
+        },
+        "Linux": {
+            "family": "Roboto",
+            "size": 13,
+            "weight": "normal"
+        }
     }
-  }
 }
diff --git a/ms2rescore/plotting.py b/ms2rescore/plotting.py
index abaff004..242668a4 100644
--- a/ms2rescore/plotting.py
+++ b/ms2rescore/plotting.py
@@ -1,4 +1,4 @@
-"""Plot MS²ReScore results."""
+"""Plot MS²Rescore results."""
 
 import logging
 import os
diff --git a/ms2rescore/rescoring_engines/mokapot.py b/ms2rescore/rescoring_engines/mokapot.py
new file mode 100644
index 00000000..64655851
--- /dev/null
+++ b/ms2rescore/rescoring_engines/mokapot.py
@@ -0,0 +1,137 @@
+"""Mokapot integration for MS²Rescore."""
+
+import logging
+from typing import Any, Dict, List, Optional
+
+import numpy as np
+import pandas as pd
+import psm_utils
+from mokapot.brew import brew
+from mokapot.dataset import LinearPsmDataset
+from pyteomics.mass import nist_mass
+
+logger = logging.getLogger(__name__)
+
+
+def rescore(
+    psm_list: psm_utils.PSMList,
+    mokapot_kwargs: Optional[Dict[str, Any]] = None,
+):
+    """
+    Rescore PSMs with Mokapot.
+
+    Parameters
+    ----------
+    psm_list
+        PSMs to be rescored.
+    mokapot_kwargs
+        Additional keyword arguments for Mokapot. Defaults to ``None``.
+
+    """
+    # Convert PSMList to Mokapot dataset
+    feature_names = psm_list[0].rescoring_features.keys()
+    lin_psm_data = convert_psm_list(psm_list, feature_names)
+
+    # Rescore
+    confidence_results, model = brew(lin_psm_data, **mokapot_kwargs)
+
+    # Reshape confidence estimates to match PSMList
+    mokapot_values_targets = (
+        confidence_results.confidence_estimates["psms"]
+        .set_index("index")
+        .sort_index()[["mokapot score", "mokapot q-value", "mokapot PEP"]]
+    )
+    mokapot_values_decoys = (
+        confidence_results.decoy_confidence_estimates["psms"]
+        .set_index("index")
+        .sort_index()[["mokapot score", "mokapot q-value", "mokapot PEP"]]
+    )
+    q = np.full((len(psm_list), 3), np.nan)
+    q[mokapot_values_targets.index] = mokapot_values_targets.values
+    q[mokapot_values_decoys.index] = mokapot_values_decoys.values
+
+    # Add Mokapot results to PSMList
+    psm_list["score"] = q[:, 0]
+    psm_list["qvalue"] = q[:, 1]
+    psm_list["pep"] = q[:, 2]
+
+
+def convert_psm_list(
+    psm_list: psm_utils.PSMList,
+    feature_names: List[str],
+    keep_lower_rank_psms: bool = False,
+) -> LinearPsmDataset:
+    """
+    Convert a PSM list to a Mokapot dataset.
+
+    Parameters
+    ----------
+    psm_list
+        PSMList to rescore.
+    feature_names
+        List of feature names to use. Items must be keys in the PSM `rescoring_features` dict.
+    keep_lower_rank_psms
+        If ``True``, keep all PSMs with rank <= 2. Defaults to ``False``.
+
+    Returns
+    -------
+    mokapot.dataset.LinearPsmDataset
+
+    """
+    if None in psm_list["rank"]:
+        psm_list.set_ranks()
+
+    psm_df = psm_list.to_dataframe()
+    psm_df = psm_df.reset_index(drop=True).reset_index()
+    if not keep_lower_rank_psms:
+        psm_df = psm_df[psm_df["rank"] == 1]
+
+    psm_df["peptide"] = (
+        psm_df["peptidoform"].astype(str).str.replace(r"(/\d+$)", "", n=1, regex=True)
+    )
+    psm_df["is_target"] = ~psm_df["is_decoy"]
+    psm_df["charge"] = psm_df["peptidoform"].apply(lambda x: x.precursor_charge)
+    psm_df["calcmass"] = psm_df["peptidoform"].apply(lambda x: x.theoretical_mass)
+    psm_df["expmass"] = _mz_to_mass(psm_df["precursor_mz"], psm_df["charge"])
+    psm_df = pd.concat(
+        [
+            psm_df.drop(columns=["rescoring_features"]),
+            pd.DataFrame(list(psm_df["rescoring_features"])).fillna(0.0),
+        ],
+        axis=1,
+    )
+
+    required_columns = [
+        "index",
+        "peptide",
+        "is_target",
+        "protein_list",
+        "run",
+        "calcmass",
+        "expmass",
+        "retention_time",
+        "charge",
+    ]
+    required_columns.extend(feature_names)
+
+    lin_psm_data = LinearPsmDataset(
+        psms=psm_df[required_columns],
+        target_column="is_target",
+        spectrum_columns="index",  # Use artificial index to allow multi-rank rescoring
+        peptide_column="peptide",
+        protein_column="protein_list",
+        feature_columns=feature_names,
+        filename_column="run",
+        scan_column="index",  # Keep as spectrum_id?
+        calcmass_column="calcmass",
+        expmass_column="expmass",
+        rt_column="retention_time",
+        charge_column="charge",
+    )
+
+    return lin_psm_data
+
+
+def _mz_to_mass(mz: float, charge: int) -> float:
+    """Convert m/z to mass."""
+    return mz * charge - charge * nist_mass["H"][1][0]
diff --git a/ms2rescore/rescoring_engines/percolator.py b/ms2rescore/rescoring_engines/percolator.py
index e122eb81..790ad4e2 100644
--- a/ms2rescore/rescoring_engines/percolator.py
+++ b/ms2rescore/rescoring_engines/percolator.py
@@ -116,7 +116,7 @@ def _update_psm_scores(psm_list: psm_utils.PSMList, target_pout: str, decoy_pout
 
 
 def _write_pin_file(psm_list: psm_utils.PSMList, filepath: str):
-    """Write PIN file for rescoring"""
+    """Write PIN file for rescoring."""
     logger.debug(f"Writing PIN file to {filepath}")
     psm_utils.io.write_file(
         psm_list,
diff --git a/pyproject.toml b/pyproject.toml
index 35756cfd..9663a8c8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,6 +45,7 @@ dependencies = [
     "tomlkit",
     "psm_utils>=0.3",
     "customtkinter>=5,<6",
+    "mokapot>=0.9",
 ]
 
 [project.optional-dependencies]