diff --git a/.cookietemple.yml b/.cookietemple.yml
index 0359ed3..a386290 100644
--- a/.cookietemple.yml
+++ b/.cookietemple.yml
@@ -15,5 +15,5 @@ full_name: Victor Giurcoiu
 email: victor.giurcoiu@tum.de
 project_name: spectrum_fundamentals
 project_short_description: Fundamentals public repo
-version: 0.5.2
+version: 0.7.8
 license: MIT
diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
index 9ae5f09..902c9de 100644
--- a/.github/release-drafter.yml
+++ b/.github/release-drafter.yml
@@ -1,5 +1,5 @@
-name-template: "0.5.2 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.5.2 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.7.8 " # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.7.8 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 
diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml
index f9d2ff1..0dd9cb6 100644
--- a/.github/workflows/build_package.yml
+++ b/.github/workflows/build_package.yml
@@ -9,14 +9,14 @@ jobs:
         strategy:
             matrix:
                 os: [macos-latest, ubuntu-latest, windows-latest]
-                python: [3.8, 3.9]
+                python: ["3.9", "3.10"]
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
                   python-version: ${{ matrix.python }}
 
diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml
index 8ea1f8f..825aa6f 100644
--- a/.github/workflows/labeler.yml
+++ b/.github/workflows/labeler.yml
@@ -11,7 +11,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.3.3
+              uses: actions/checkout@v4
 
             - name: Run Labeler
               uses: crazy-max/ghaction-github-labeler@v5.0.0
diff --git a/.github/workflows/main_master_branch_protection.yml b/.github/workflows/main_master_branch_protection.yml
index 0f9fb66..8619c3a 100644
--- a/.github/workflows/main_master_branch_protection.yml
+++ b/.github/workflows/main_master_branch_protection.yml
@@ -40,9 +40,9 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Set up Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
-                  python-version: "3.8"
+                  python-version: "3.9"
             # PRs to the repository master branch are only ok if coming from any patch or release branch
             - name: Install mlf-core
               run: pip install mlf-core
diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml
index 6f00229..bf649a2 100644
--- a/.github/workflows/publish_docs.yml
+++ b/.github/workflows/publish_docs.yml
@@ -7,13 +7,13 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
-                  python-version: 3.8
+                  python-version: 3.9
 
             - name: Install pip
               run: |
@@ -30,7 +30,7 @@ jobs:
 
             - name: Deploy
               if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main'}}
-              uses: peaceiris/actions-gh-pages@v3
+              uses: peaceiris/actions-gh-pages@v4
               with:
                   github_token: ${{ secrets.GITHUB_TOKEN }}
                   publish_dir: ./docs/_build/html
diff --git a/.github/workflows/publish_package.yml b/.github/workflows/publish_package.yml
index 19c7e0b..60093c0 100644
--- a/.github/workflows/publish_package.yml
+++ b/.github/workflows/publish_package.yml
@@ -10,12 +10,12 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.3.4
+              uses: actions/checkout@v4
               with:
                   fetch-depth: 2
 
             - name: Set up Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
                   python-version: "3.9"
 
@@ -29,7 +29,7 @@ jobs:
                   poetry build --ansi
 
             - name: Publish package on PyPI
-              uses: pypa/gh-action-pypi-publish@v1.8.14
+              uses: pypa/gh-action-pypi-publish@v1.10.3
               with:
                   # TODO COOKIETEMPLE: Configure your PyPI Token to enable automatic deployment to PyPi on releases
                   # https://help.github.com/en/actions/configuring-and-managing-workflows/creating-and-storing-encrypted-secrets
diff --git a/.github/workflows/release_drafter.yml b/.github/workflows/release_drafter.yml
index 41f8209..46853d2 100644
--- a/.github/workflows/release_drafter.yml
+++ b/.github/workflows/release_drafter.yml
@@ -14,6 +14,6 @@ jobs:
     update_release_draft:
         runs-on: ubuntu-latest
         steps:
-            - uses: release-drafter/release-drafter@v5
+            - uses: release-drafter/release-drafter@v6
               env:
                   GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
diff --git a/.github/workflows/run_cookietemple_lint.yml b/.github/workflows/run_cookietemple_lint.yml
index c3d0fbc..1af37d3 100644
--- a/.github/workflows/run_cookietemple_lint.yml
+++ b/.github/workflows/run_cookietemple_lint.yml
@@ -7,11 +7,11 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
                   python-version: 3.9
 
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index 63040a2..080d0c4 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -19,47 +19,47 @@ jobs:
             matrix:
                 include:
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "pre-commit",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "safety",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "mypy",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: windows-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: macos-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "typeguard",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "xdoctest",
                       }
                     - {
-                          python-version: 3.8,
+                          python-version: 3.9,
                           os: ubuntu-latest,
                           session: "docs-build",
                       }
@@ -69,10 +69,10 @@ jobs:
 
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.3.4
+              uses: actions/checkout@v4
 
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
                   python-version: ${{ matrix.python-version }}
 
@@ -116,15 +116,16 @@ jobs:
               run: nox --force-color --python=${{ matrix.python-version }}
 
             - name: Upload coverage data
-              if: always() && matrix.session == 'tests'
-              uses: actions/upload-artifact@v3
+              if: always() && matrix.session == 'tests' && matrix.os == 'ubuntu-latest'
+              uses: actions/upload-artifact@v4
               with:
+                  include-hidden-files: "true"
                   name: coverage-data
                   path: ".coverage.*"
 
             - name: Upload documentation
               if: matrix.session == 'docs-build'
-              uses: actions/upload-artifact@v3
+              uses: actions/upload-artifact@v4
               with:
                   name: docs
                   path: docs/_build
@@ -134,12 +135,12 @@ jobs:
         needs: tests
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
 
-            - name: Set up Python 3.8
-              uses: actions/setup-python@v5.1.0
+            - name: Set up Python 3.9
+              uses: actions/setup-python@v5.2.0
               with:
-                  python-version: 3.8
+                  python-version: 3.9
 
             - name: Install Poetry
               run: |
@@ -154,7 +155,7 @@ jobs:
                   nox --version
 
             - name: Download coverage data
-              uses: actions/download-artifact@v3
+              uses: actions/download-artifact@v4
               with:
                   name: coverage-data
 
@@ -165,4 +166,4 @@ jobs:
               run: nox --force-color --session=coverage -- xml -i
 
             - name: Upload coverage report
-              uses: codecov/codecov-action@v3.1.1
+              uses: codecov/codecov-action@v4.6.0
diff --git a/.github/workflows/sync_project.yml b/.github/workflows/sync_project.yml
index e0f4e02..111650e 100644
--- a/.github/workflows/sync_project.yml
+++ b/.github/workflows/sync_project.yml
@@ -10,14 +10,14 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Setup Python
-              uses: actions/setup-python@v5.1.0
+              uses: actions/setup-python@v5.2.0
               with:
-                  python-version: 3.8
+                  python-version: 3.9
 
             - name: Install cookietemple
               run: pip install cookietemple
 
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
               with:
                   fetch-depth: 0
                   token: "${{ secrets.CT_SYNC_TOKEN }}"
diff --git a/README.rst b/README.rst
index 4d3c9f5..178a09c 100644
--- a/README.rst
+++ b/README.rst
@@ -1,5 +1,5 @@
-spectrum_fundamentals
-===========================
+Spectrum Fundamentals
+=====================
 
 |PyPI| |Python Version| |License| |Read the Docs| |Build| |Tests| |Codecov| |pre-commit| |Black|
 
@@ -13,15 +13,15 @@ spectrum_fundamentals
    :target: https://opensource.org/licenses/MIT
    :alt: License
 .. |Read the Docs| image:: https://img.shields.io/readthedocs/spectrum_fundamentals/latest.svg?label=Read%20the%20Docs
-   :target: https://spectrum_fundamentals.readthedocs.io/
-   :alt: Read the documentation at https://spectrum_fundamentals.readthedocs.io/
+   :target: https://spectrum-fundamentals.readthedocs.io/
+   :alt: Read the documentation at https://spectrum-fundamentals.readthedocs.io/
 .. |Build| image:: https://github.com/wilhelm-lab/spectrum_fundamentals/workflows/Build%20spectrum_fundamentals%20Package/badge.svg
    :target: https://github.com/wilhelm-lab/spectrum_fundamentals/actions?workflow=Package
    :alt: Build Package Status
 .. |Tests| image:: https://github.com/wilhelm-lab/spectrum_fundamentals/workflows/Run%20spectrum_fundamentals%20Tests/badge.svg
    :target: https://github.com/wilhelm-lab/spectrum_fundamentals/actions?workflow=Tests
    :alt: Run Tests Status
-.. |Codecov| image:: https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals/branch/master/graph/badge.svg
+.. |Codecov| image:: https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals
    :alt: Codecov
 .. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
@@ -31,37 +31,10 @@ spectrum_fundamentals
    :target: https://github.com/psf/black
    :alt: Black
 
+spectrum_fundamentals is a package primarily developed for usage within the rescoring and spectral library generation pipeline oktoberfest (https://github.com/wilhelm-lab/oktoberfest).
 
-Features
---------
-
-* TODO
-
-
-Installation
-------------
-
-You can install *spectrum_fundamentals* via pip_ from PyPI_:
-
-.. code:: console
-
-   $ pip install spectrum_fundamentals
-
-
-Usage
------
-
-Please see the `Command-line Reference <Usage_>`_ for details.
-
-
-Credits
--------
-
-This package was created with cookietemple_ using Cookiecutter_ based on Hypermodern_Python_Cookiecutter_.
-
-.. _cookietemple: https://cookietemple.com
-.. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _PyPI: https://pypi.org/
-.. _Hypermodern_Python_Cookiecutter: https://github.com/cjolowicz/cookiecutter-hypermodern-python
-.. _pip: https://pip.pypa.io/
-.. _Usage: https://spectrum_fundamentals.readthedocs.io/en/latest/usage.html
+It provides the following functionalities:
+ -  conversion between search engine-specific modstrings and the ProForma standard
+ -  calculation of theoretical peptide / ion masses
+ -  annotation of spectra
+ -  spectral similarity calculation with various metrics
diff --git a/ReadMe.md b/ReadMe.md
index d19ba87..31d54ff 100644
--- a/ReadMe.md
+++ b/ReadMe.md
@@ -1,35 +1,30 @@
-# Spectrum Fundamentals
-
-Spectrum Fundamentals is a package we use in our rescoring pipeline. It was created to be able to handle spectra from different files.
-
-## Features
+[![PyPI](https://img.shields.io/pypi/v/spectrum_fundamentals.svg)](https://pypi.org/project/spectrum_fundamentals/)
+[![Python Version](https://img.shields.io/pypi/pyversions/spectrum_fundamentals)](https://pypi.org/project/spectrum_fundamentals)
+[![License](https://img.shields.io/github/license/wilhelm-lab/spectrum_fundamentals)](https://opensource.org/licenses/MIT)
+[![Read the Docs](https://img.shields.io/readthedocs/spectrum_fundamentals/latest.svg?label=Read%20the%20Docs)](https://spectrum-fundamentals.readthedocs.io/)
+[![Build](https://github.com/wilhelm-lab/spectrum_fundamentals/workflows/Build%20spectrum_fundamentals%20Package/badge.svg)](https://github.com/wilhelm-lab/spectrum_fundamentals/actions?workflow=Package)
+[![Tests](https://github.com/wilhelm-lab/spectrum_fundamentals/workflows/Run%20spectrum_fundamentals%20Tests/badge.svg)](https://github.com/wilhelm-lab/spectrum_fundamentals/actions?workflow=Tests)
+[![Codecov](https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals/branch/main/graph/badge.svg)](https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
--   Annotate Spectra.
--   Modify peptide sequence to follow one of the recommended notations of ProForma.
--   Generate features than can be used by percoltor for rescoring (spectral angle, cosine similarity, Pearson's correlation, Spearman's correlation, etc.).
-
-## Installation
-
-Install with:
+# Spectrum Fundamentals
 
-```
-pip install git+https://github.com/wilhelm-lab/spectrum_fundamentals
-```
+spectrum_fundamentals is a package primarily developed for usage within the rescoring and spectral library generation pipeline oktoberfest (https://github.com/wilhelm-lab/oktoberfest).
 
-## Usage
+It provides the following functionalities:
 
-### Annotation Pipeline
+-   conversion between search engine-specific modstrings and the ProForma standard
+-   calculation of theoretical peptide / ion masses
+-   annotation of spectra
+-   spectral similarity calculation with various metrics
 
-The annotation script can be found in the package in annotation/annotation.py.
+## Documentation
 
--   Install and import the function:
+The official documentation can be found at https://spectrum-fundamentals.readthedocs.io
 
-```
-from spectrum_fundamentals.annotation.annotation import annotate_spectra
-```
+## How to cite
 
--   Apply the function on any given dataframe with peptides meta data, raw intensities and mz:
+Please always cite the main publication:
 
-```
-annotate_spectra(dataframe)
-```
+[Oktoberfest] Picciani M, Gabriel W, Giurcoiu VG et al. (2023), _Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit_, [Proteomics](https://doi.org/10.1002/pmic.202300112)
diff --git a/cookietemple.cfg b/cookietemple.cfg
index 4271a2c..e174cfc 100644
--- a/cookietemple.cfg
+++ b/cookietemple.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.2
+current_version = 0.7.8
 
 [bumpversion_files_whitelisted]
 init_file = spectrum_fundamentals/__init__.py
diff --git a/docs/API.rst b/docs/API.rst
new file mode 100644
index 0000000..8888eae
--- /dev/null
+++ b/docs/API.rst
@@ -0,0 +1,33 @@
+.. module:: spectrum_fundamentals
+
+.. automodule:: spectrum_fundamentals
+   :noindex:
+
+API
+===
+
+Import spectrum_fundamentals using
+
+.. code-block:: python
+
+   import spectrum_fundamentals as specfun
+
+
+Modstring conversions: :code:`convert`
+--------------------------------------
+
+
+Peptide and ion mass / mz calculations: :code:`peptide`
+-------------------------------------------------------
+
+
+Annotation of spectra: :code:`annot`
+------------------------------------
+
+
+Spectral similarity calculation: :code:`similarity`
+---------------------------------------------------
+
+
+Further utility functions: :code:`utils`
+----------------------------------------
\ No newline at end of file
diff --git a/docs/_key_contributors.rst b/docs/_key_contributors.rst
new file mode 100644
index 0000000..20e1b6f
--- /dev/null
+++ b/docs/_key_contributors.rst
@@ -0,0 +1,22 @@
+.. sidebar:: Key Contributors
+
+   Current developers
+
+   * `Arne van den Berg <https://github.com/arne-vdb>`_
+   * `Wassim Gabriel <https://github.com/WassimG>`_
+   * `Victor-George Giurcoiu <https://github.com/victorgiurcoiu>`_
+   * `Firas Hamood <https://github.com/fhamood>`_
+   * `Cecilia Jensen`_
+   * `Mostafa Kalhor <https://github.com/mostafakalhor>`_
+   * `Ludwig Lautenbacher <https://github.com/LLautenbacher>`_
+   * `Julian Mueller <https://github.com/jmueller95>`_
+   * `Mario Picciani <https://github.com/picciama>`_
+   * `Ayla Schröder <https://github.com/ayla-s>`_
+   * `Omar Shouman <https://github.com/omsh>`_
+   * `Armin Soleymaniniya <https://github.com/arminsl>`_
+   * `Matthew The <https://github.com/MatthewThe>`_
+   * `Zixuan Xiao <https://github.com/zix-xiao>`_
+
+   Other roles
+
+   * `Mathias Wilhelm <https://github.com/mwilhelm42>`_ advisor and PI of wilhelmlab
\ No newline at end of file
diff --git a/docs/_static/custom_cookietemple.css b/docs/_static/custom_cookietemple.css
index c286236..553419b 100644
--- a/docs/_static/custom_cookietemple.css
+++ b/docs/_static/custom_cookietemple.css
@@ -1,6 +1,80 @@
 @import "basic.css";
 
-/*Set max width to none so the theme uses all available width*/
 .wy-nav-content {
-    max-width: none;
+    max-width: 1200px;
+}
+
+.wy-side-nav-search {
+    background-color: inherit;
+}
+
+table.align-default {
+    text-align: left;
+}
+
+.fixed-table th:first-child,
+.fixed-table td:first-child,
+.autosummary th:first-child,
+.autosummary td:first-child {
+    min-width: 250px;
+}
+
+.autosummary th:first-child,
+.autosummary td:first-child {
+    min-width: 400px;
+}
+
+.fixed-table th:last-child,
+.fixed-table td:last-child,
+.autosummary th:last-child,
+.autosummary td:last-child {
+    width: 100%;
+}
+
+.fixed-table {
+    margin-left: 0;
+}
+
+.wy-table-responsive table th p,
+.wy-table-responsive table td p {
+    white-space: normal;
+}
+
+.autosummary {
+    margin-left: 0 !important;
+}
+
+.main-config-table tbody tr:nth-child(n + 4):nth-child(-n + 5) td:nth-child(1) {
+    padding-left: 50px;
+}
+
+.main-config-table tbody tr:nth-child(n + 7):nth-child(-n + 7) td:nth-child(1) {
+    padding-left: 50px;
+}
+
+.lib-rescore-config-table
+    tbody
+    tr:nth-child(n + 2):nth-child(-n + 5)
+    td:nth-child(1) {
+    padding-left: 50px;
+}
+
+.lib-rescore-config-table tbody tr:nth-last-child(-n + 2) td:nth-child(1) {
+    padding-left: 50px;
+}
+
+.lib-config-table tbody tr:nth-child(n + 2):nth-child(-n + 3) td:nth-child(1) {
+    padding-left: 50px;
+}
+
+.lib-config-table tbody tr:nth-last-child(-n + 6) td:nth-child(1) {
+    padding-left: 50px;
+}
+
+.digest-config-table tbody tr:not(:first-child) td:nth-child(1) {
+    padding-left: 50px;
+}
+
+.date {
+    font-size: 50%;
 }
diff --git a/docs/authors.rst b/docs/authors.rst
deleted file mode 100644
index f68a337..0000000
--- a/docs/authors.rst
+++ /dev/null
@@ -1,13 +0,0 @@
-=======
-Credits
-=======
-
-Development Lead
-----------------
-
-* Victor Giurcoiu <victor.giurcoiu@tum.de>
-
-Contributors
-------------
-
-None yet. Why not be the first?
diff --git a/docs/code_of_conduct.rst b/docs/code_of_conduct.rst
deleted file mode 100644
index 96e0ba2..0000000
--- a/docs/code_of_conduct.rst
+++ /dev/null
@@ -1 +0,0 @@
-.. include:: ../CODE_OF_CONDUCT.rst
diff --git a/docs/conf.py b/docs/conf.py
index 6d98a8a..0d12982 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 # mypy: ignore-errors
-# pre-commit: ignore-errors
 # spectrum_fundamentals documentation build configuration file
 #
 # If extensions (or modules to document with autodoc) are in another
@@ -8,18 +7,16 @@
 # relative to the documentation root, use os.path.abspath to make it
 # absolute, like shown here.
 #
-import importlib
 import inspect
 import os
-import re
-import subprocess
 import sys
-from typing import Any
+from datetime import datetime
+from pathlib import Path
 
-sys.path.insert(0, os.path.abspath(".."))
+from jinja2.defaults import DEFAULT_FILTERS
 
+sys.path.insert(0, os.path.abspath(".."))
 
-# -- General configuration ---------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
 # needs_sphinx = '1.0'
@@ -30,8 +27,9 @@
 # Add 'sphinx_automodapi.automodapi' if you want to build modules
 extensions = [
     "sphinx.ext.autodoc",
-    "sphinx.ext.napoleon",
-    "sphinx.ext.linkcode",
+    "sphinx.ext.autosummary",
+    "sphinx_autodoc_typehints",
+    "sphinx.ext.intersphinx",
     "sphinx_click",
 ]
 
@@ -45,25 +43,25 @@
 master_doc = "index"
 
 # General information about the project.
-project = "spectrum_fundamentals"
-copyright = "2022, Victor Giurcoiu"
-author = "Victor Giurcoiu"
+project = "Spectrum-IO"
+author = "Oktoberfest development team"
+copyright = f"{datetime.now():%Y}, Wilhelmlab at Technical University of Munich"
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
 # the built documents.
 #
 # The short X.Y version.
-version = "0.5.2"
+version = "0.7.8"
 # The full version, including alpha/beta/rc tags.
-release = "0.5.2"
+release = "0.7.8"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -76,9 +74,21 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
+suppress_warnings = [
+    "ref.citation",
+]
 
 # -- Options for HTML output -------------------------------------------
 
+html_context = {
+    "display_github": True,  # Integrate GitHub
+    "github_user": "wilhelm-lab",  # Username
+    "github_repo": "spectrum_fundamentals",  # Repo name
+    "github_version": "development",  # Version
+    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
+    "github_url": "https://github.com/wilhelm-lab/spectrum_fundamentals/",
+}
+
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
@@ -88,7 +98,12 @@
 # theme further.  For a list of options available for each theme, see the
 # documentation.
 #
-# html_theme_options = {}
+html_theme_options = dict(
+    navigation_depth=4,
+    logo_only=True,
+)
+# html_logo = "_static/img/Oktoberfest.svg"
+
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -99,8 +114,7 @@
 # -- Options for HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "spectrum_fundamentalsdoc"
-
+htmlhelp_basename = "spectrumfundamentalsdoc"
 
 # -- Options for LaTeX output ------------------------------------------
 
@@ -125,14 +139,13 @@
 latex_documents = [
     (
         master_doc,
-        "spectrum_fundamentals.tex",
-        "spectrum_fundamentals Documentation",
-        "Victor Giurcoiu",
+        "SpectrumFundamentals.tex",
+        "SpectrumFundamentals Documentation",
+        author,
         "manual",
     ),
 ]
 
-
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
@@ -140,8 +153,8 @@
 man_pages = [
     (
         master_doc,
-        "spectrum_fundamentals",
-        "spectrum_fundamentals Documentation",
+        "SpectrumFundamentals",
+        "SpectrumFundamentals Documentation",
         [author],
         1,
     )
@@ -158,10 +171,10 @@
 texinfo_documents = [
     (
         master_doc,
-        "spectrum_fundamentals",
-        "spectrum_fundamentals Documentation",
+        "SpectrumFundamentals",
+        "SpectrumFundamentals Documentation",
         author,
-        "spectrum_fundamentals",
+        "SpectrumFundamentals",
         "One line description of project.",
         "Miscellaneous",
     ),
@@ -170,65 +183,67 @@
 html_css_files = [
     "custom_cookietemple.css",
 ]
+# -- Options for intersphinx mappings ----------------------------------
+
+intersphinx_mapping = dict(
+    matplotlib=("https://matplotlib.org/stable/", None),
+    numpy=("https://numpy.org/doc/stable/", None),
+    pandas=("https://pandas.pydata.org/pandas-docs/stable/", None),
+    python=("https://docs.python.org/3", None),
+    scipy=("https://docs.scipy.org/doc/scipy/", None),
+    seaborn=("https://seaborn.pydata.org/", None),
+    sklearn=("https://scikit-learn.org/stable/", None),
+)
 
-html_context = {
-    "display_github": True,  # Integrate GitHub
-    "github_user": "wilhelm-lab",  # Username
-    "github_repo": "spectrum_fundamentals",  # Repo name
-    "github_version": "main",  # Version
-    "conf_py_path": "/spectrum_fundamentals/",  # Path in the checkout to the docs root
-    "github_url": "https://github.com/wilhelm-lab/spectrum_fundamentals/",
-}
 
-repository_url = "https://github.com/wilhelm-lab/spectrum_fundamentals"
+# module path filter to create direct links to sources for autogenerated docs
+# according to https://gist.github.com/flying-sheep/b65875c0ce965fbdd1d9e5d0b9851ef1
 
-# Linkcode config
 
+def get_obj_module(qualname):
+    """Get a module/class/attribute and its original module by qualname."""
+    modname = qualname
+    classname = None
+    attrname = None
+    while modname not in sys.modules:
+        attrname = classname
+        modname, classname = modname.rsplit(".", 1)
 
-def git(*args):
-    """Gets git linkcode."""
-    return subprocess.check_output(["git", *args]).strip().decode()
+    # retrieve object and find original module name
+    if classname:
+        cls = getattr(sys.modules[modname], classname)
+        modname = cls.__module__
+        obj = getattr(cls, attrname) if attrname else cls
+    else:
+        obj = None
 
+    return obj, sys.modules[modname]
 
-# https://github.com/DisnakeDev/disnake/blob/7853da70b13fcd2978c39c0b7efa59b34d298186/docs/conf.py#L192
-# Current git reference. Uses branch/tag name if found, otherwise uses commit hash
-git_ref = None
-try:
-    git_ref = git("name-rev", "--name-only", "--no-undefined", "HEAD")
-    git_ref = re.sub(r"^(remotes/[^/]+|tags)/", "", git_ref)
-except Exception:
-    print()
 
-# (if no name found or relative ref, use commit hash instead)
-if not git_ref or re.search(r"[\^~]", git_ref):
+def get_linenos(obj):
+    """Get an object’s line numbers."""
     try:
-        git_ref = git("rev-parse", "HEAD")
-    except Exception:
-        git_ref = "main"
+        lines, start = inspect.getsourcelines(obj)
+    except TypeError:  # obj is an attribute or None
+        return None, None
+    else:
+        return start, start + len(lines) - 1
 
-# https://github.com/DisnakeDev/disnake/blob/7853da70b13fcd2978c39c0b7efa59b34d298186/docs/conf.py#L192
-_module_path = os.path.dirname(importlib.util.find_spec("spectrum_fundamentals").origin)  # type: ignore
 
+project_dir = Path(__file__).parent.parent  # project/docs/conf.py/../.. → project/
+github_url = "https://github.com/{github_user}/{github_repo}/tree/{github_version}".format_map(html_context)
 
-def linkcode_resolve(domain, info):
-    """Resolves linkcode."""
-    if domain != "py":
-        return None
 
-    try:
-        obj: Any = sys.modules[info["module"]]
-        for part in info["fullname"].split("."):
-            obj = getattr(obj, part)
-        obj = inspect.unwrap(obj)
-
-        if isinstance(obj, property):
-            obj = inspect.unwrap(obj.fget)  # type: ignore
-
-        path = os.path.relpath(inspect.getsourcefile(obj), start=_module_path)  # type: ignore
-        src, lineno = inspect.getsourcelines(obj)
-    except Exception:
-        return None
-
-    path = f"{path}#L{lineno}-L{lineno + len(src) - 1}"
-    git_ref = "documentation"
-    return f"{repository_url}/blob/{git_ref}/spectrum_fundamentals/{path}"
+def modurl(qualname):
+    """Get the full GitHub URL for some object’s qualname."""
+    obj, module = get_obj_module(qualname)
+    path = Path(module.__file__).relative_to(project_dir)
+    start, end = get_linenos(obj)
+    fragment = f"#L{start}-L{end}" if start and end else ""
+    return f"{github_url}/{path}{fragment}"
+
+
+# html_context doesn’t apply to autosummary templates ☹
+# and there’s no way to insert filters into those templates
+# so we have to modify the default filters
+DEFAULT_FILTERS["modurl"] = modurl
diff --git a/docs/contributing.rst b/docs/contributing.rst
index 713ff34..f63fb64 100644
--- a/docs/contributing.rst
+++ b/docs/contributing.rst
@@ -14,7 +14,7 @@ Here is a list of important resources for contributors:
 
 .. _MIT license: https://opensource.org/licenses/MIT
 .. _Source Code: https://github.com/wilhelm-lab/spectrum_fundamentals
-.. _Documentation: https://spectrum_fundamentals.readthedocs.io/
+.. _Documentation: https://spectrum-fundamentals.readthedocs.io/
 .. _Issue Tracker: https://github.com/wilhelm-lab/spectrum_fundamentals/issues
 
 How to report a bug
@@ -32,7 +32,7 @@ Request features on the `Issue Tracker`_.
 How to set up your development environment
 ------------------------------------------
 
-You need Python 3.8+ and the following tools:
+You need Python 3.9+ and the following tools:
 
 - Poetry_
 - Nox_
diff --git a/docs/index.rst b/docs/index.rst
index 8cfd4a4..834c569 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -1,23 +1,25 @@
-.. include:: ../README.rst
-===========================
-Welcome to spectrum_fundamentals's documentation!
-==========================================================
+.. include:: readme.rst
+
+.. include:: _key_contributors.rst
+
+.. role:: small
+
+.. role:: smaller
+
+.. include:: quickstart.rst
+
+.. include:: news.rst
 
 .. toctree::
+   :hidden:
    :maxdepth: 2
    :caption: Contents:
 
-   readme
    installation
    usage
-   reference
+   API
    contributing
-   authors
-   code_of_conduct
-   modules
-
-Indices and tables
-==================
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+   reference
+
+.. _github: https://github.com/wilhelm-lab/spectrum_fundamentals
+
diff --git a/docs/installation.rst b/docs/installation.rst
index 9a524d2..7fc10c1 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -1,53 +1,12 @@
 .. highlight:: shell
 
-============
 Installation
 ============
 
+spectrum_fundamentals is listed on the Python Package Index (PyPI) and can be installed with pip.
 
-Stable release
---------------
-
-To install spectrum_fundamentals, run this command in your terminal:
-
-.. code-block:: console
-
-    $ pip install spectrum_fundamentals
-
-This is the preferred method to install spectrum_fundamentals, as it will always install the most recent stable release.
-
-If you don't have `pip`_ installed, this `Python installation guide`_ can guide
-you through the process.
-
-.. _pip: https://pip.pypa.io
-.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
-
-
-From sources
-------------
-
-The sources for spectrum_fundamentals can be downloaded from the `Github repo`_.
-Please note that you require `poetry`_ to be installed.
-
-You can either clone the public repository:
-
-.. code-block:: console
-
-    $ git clone git://github.com/wilhelm-lab/spectrum_fundamentals
-
-Or download the `tarball`_:
-
-.. code-block:: console
-
-    $ curl -OJL https://github.com/wilhelm-lab/spectrum_fundamentals/tarball/master
-
-Once you have a copy of the source, you can install it with:
-
-.. code-block:: console
+.. code-block:: bash
 
-    $ make install
+   pip install spectrum_fundamentals
 
 
-.. _Github repo: https://github.com/wilhelm-lab/spectrum_fundamentals
-.. _tarball: https://github.com/wilhelm-lab/spectrum_fundamentals/tarball/master
-.. _poetry: https://python-poetry.org/
diff --git a/docs/modules.rst b/docs/modules.rst
deleted file mode 100644
index eee8b55..0000000
--- a/docs/modules.rst
+++ /dev/null
@@ -1,9 +0,0 @@
-spectrum_fundamentals
-=================
-
-.. toctree::
-   :maxdepth: 4
-
-   spectrum_fundamentals
-   spectrum_fundamentals.annotation
-   spectrum_fundamentals.metrics
diff --git a/docs/news.rst b/docs/news.rst
new file mode 100644
index 0000000..a4057fe
--- /dev/null
+++ b/docs/news.rst
@@ -0,0 +1,5 @@
+News
+====
+
+.. role:: date
+    :class: date
\ No newline at end of file
diff --git a/docs/quickstart.rst b/docs/quickstart.rst
new file mode 100644
index 0000000..25b5d75
--- /dev/null
+++ b/docs/quickstart.rst
@@ -0,0 +1,7 @@
+Quickstart
+----------
+
+-  Discuss usage, development and issues on `GitHub <https://github.com/wilhelm-lab/spectrum_fundamentals>`_.
+-  Check the `usage principles <./usage.html>`_ or the `API <./API.html>`_.
+-  Check the `Contributor Guide <./contributing.html>`_ if you want to participate in developing.
+-  Consider citing the main publication, `Oktoberfest <https://doi.org/10.1002/pmic.202300112>`_.
\ No newline at end of file
diff --git a/docs/reference.rst b/docs/reference.rst
index bdc40a9..0323c01 100644
--- a/docs/reference.rst
+++ b/docs/reference.rst
@@ -1,10 +1,8 @@
-Reference
-=========
+How to cite
+===========
 
-.. contents::
-    :local:
-    :backlinks: none
+If you want to cite spectrum_fundamentals in your work, please cite the main Oktoberfest publication:
 
-
-.. automodule:: spectrum_fundamentals.__main__
-   :members:
+.. [1] Picciani M, Gabriel W, Giurcoiu VG et al. (2023),
+    *Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit*,
+    `Proteomics <https://doi.org/10.1002/pmic.202300112>`__.
\ No newline at end of file
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 8c8b0a9..3c8d7e7 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,7 +1 @@
-Sphinx>=4.0.1
-sphinx_rtd_theme>=0.5.2
-sphinx-rtd-dark-mode>=1.2.1
-sphinx-automodapi>=0.13
-sphinx_click>=3.0.0
-click>=8.0.1
--r ../requirements.txt
\ No newline at end of file
+-r ../requirements.txt
diff --git a/docs/spectrum_fundamentals.annotation.rst b/docs/spectrum_fundamentals.annotation.rst
deleted file mode 100644
index a88d8c0..0000000
--- a/docs/spectrum_fundamentals.annotation.rst
+++ /dev/null
@@ -1,21 +0,0 @@
-spectrum\_fundamentals.annotation package
-=========================================
-
-Submodules
-----------
-
-spectrum\_fundamentals.annotation.annotation module
----------------------------------------------------
-
-.. automodule:: spectrum_fundamentals.annotation.annotation
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: spectrum_fundamentals.annotation
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/spectrum_fundamentals.metrics.rst b/docs/spectrum_fundamentals.metrics.rst
deleted file mode 100644
index ee23211..0000000
--- a/docs/spectrum_fundamentals.metrics.rst
+++ /dev/null
@@ -1,45 +0,0 @@
-spectrum\_fundamentals.metrics package
-======================================
-
-Submodules
-----------
-
-spectrum\_fundamentals.metrics.fragments\_ratio module
-------------------------------------------------------
-
-.. automodule:: spectrum_fundamentals.metrics.fragments_ratio
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-spectrum\_fundamentals.metrics.metric module
---------------------------------------------
-
-.. automodule:: spectrum_fundamentals.metrics.metric
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-spectrum\_fundamentals.metrics.percolator module
-------------------------------------------------
-
-.. automodule:: spectrum_fundamentals.metrics.percolator
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-spectrum\_fundamentals.metrics.similarity module
-------------------------------------------------
-
-.. automodule:: spectrum_fundamentals.metrics.similarity
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: spectrum_fundamentals.metrics
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/spectrum_fundamentals.rst b/docs/spectrum_fundamentals.rst
deleted file mode 100644
index 66a0ac9..0000000
--- a/docs/spectrum_fundamentals.rst
+++ /dev/null
@@ -1,54 +0,0 @@
-spectrum\_fundamentals package
-==============================
-
-Subpackages
------------
-
-.. toctree::
-   :maxdepth: 4
-
-   spectrum_fundamentals.annotation
-   spectrum_fundamentals.metrics
-
-Submodules
-----------
-
-spectrum\_fundamentals.charge module
-------------------------------------
-
-.. automodule:: spectrum_fundamentals.charge
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-spectrum\_fundamentals.constants module
----------------------------------------
-
-.. automodule:: spectrum_fundamentals.constants
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-spectrum\_fundamentals.fragments module
----------------------------------------
-
-.. automodule:: spectrum_fundamentals.fragments
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-spectrum\_fundamentals.mod\_string module
------------------------------------------
-
-.. automodule:: spectrum_fundamentals.mod_string
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: spectrum_fundamentals
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/noxfile.py b/noxfile.py
index 433fb2f..e9ae0dd 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -18,12 +18,13 @@
     sys.exit(1)
 
 package = "spectrum_fundamentals"
-python_versions = ["3.8", "3.9"]
+python_versions = ["3.9", "3.10"]
 nox.options.sessions = (
     "pre-commit",
     "safety",
     "mypy",
     "tests",
+    "typeguard",
     "xdoctest",
     "docs-build",
 )
@@ -126,7 +127,7 @@ def safety(session: Session) -> None:
     """Scan dependencies for insecure packages."""
     requirements = session.poetry.export_requirements()
     session.install("safety")
-    session.run("safety", "check", "--full-report", f"--file={requirements}", "--ignore=51457")
+    session.run("safety", "check", "--full-report", f"--file={requirements}", "--ignore=51457,70612")
 
 
 @session(python=python_versions)
@@ -188,7 +189,8 @@ def docs_build(session: Session) -> None:
     """Build the documentation."""
     args = session.posargs or ["docs", "docs/_build"]
     session.install(".")
-    session.install("sphinx", "sphinx-click", "sphinx-rtd-theme", "sphinx-rtd-dark-mode")
+    session.install("sphinx", "sphinx-click", "sphinx-rtd-theme")
+    session.install("-r", "./docs/requirements.txt")
 
     build_dir = Path("docs", "_build")
     if build_dir.exists():
diff --git a/poetry.lock b/poetry.lock
index 6d66718..bc89f22 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,28 +2,47 @@
 
 [[package]]
 name = "alabaster"
-version = "0.7.13"
-description = "A configurable sidebar-enabled Sphinx theme"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.9"
 files = [
-    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
-    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
 ]
 
 [[package]]
 name = "annotated-types"
-version = "0.6.0"
+version = "0.7.0"
 description = "Reusable constraint types to use with typing.Annotated"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"},
-    {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"},
+    {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+    {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+]
+
+[[package]]
+name = "anyio"
+version = "4.4.0"
+description = "High level compatibility layer for multiple asynchronous event loop implementations"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"},
+    {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"},
 ]
 
 [package.dependencies]
-typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""}
+exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
+idna = ">=2.8"
+sniffio = ">=1.1"
+typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""}
+
+[package.extras]
+doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
+trio = ["trio (>=0.23)"]
 
 [[package]]
 name = "attrs"
@@ -46,13 +65,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p
 
 [[package]]
 name = "authlib"
-version = "1.3.0"
+version = "1.3.1"
 description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -60,30 +79,27 @@ cryptography = "*"
 
 [[package]]
 name = "babel"
-version = "2.14.0"
+version = "2.15.0"
 description = "Internationalization utilities"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-[package.dependencies]
-pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
-
 [package.extras]
 dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "bandit"
-version = "1.7.8"
+version = "1.7.9"
 description = "Security oriented static analyser for python code."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -101,33 +117,33 @@ yaml = ["PyYAML"]
 
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 python-versions = ">=3.8"
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 [package.dependencies]
@@ -147,13 +163,13 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "certifi"
-version = "2024.2.2"
+version = "2024.7.4"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [[package]]
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 description = "Python library for calculating contours of 2D quadrilateral grids"
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 [package.dependencies]
@@ -495,43 +503,38 @@ toml = ["tomli"]
 
 [[package]]
 name = "cryptography"
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 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 optional = false
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 [package.dependencies]
@@ -544,7 +547,7 @@ nox = ["nox"]
 pep8test = ["check-sdist", "click", "mypy", "ruff"]
 sdist = ["build"]
 ssh = ["bcrypt (>=3.1.5)"]
-test = ["certifi", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
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 test-randomorder = ["pytest-randomly"]
 
 [[package]]
@@ -618,13 +621,13 @@ poetry = ["poetry"]
 
 [[package]]
 name = "exceptiongroup"
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+version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -632,35 +635,35 @@ test = ["pytest (>=6)"]
 
 [[package]]
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 description = "the modular source code checker: pep8 pyflakes and co"
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 [[package]]
 name = "flake8-bandit"
@@ -679,18 +682,18 @@ flake8 = ">=5.0.0"
 
 [[package]]
 name = "flake8-bugbear"
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 [package.dependencies]
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-flake8 = ">=3.0.0"
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 [package.extras]
 dev = ["coverage", "hypothesis", "hypothesmith (>=0.2)", "pre-commit", "pytest", "tox"]
@@ -731,53 +734,53 @@ develop = ["build", "twine"]
 
 [[package]]
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 ]
 
 [package.extras]
@@ -794,15 +797,26 @@ ufo = ["fs (>=2.2.0,<3)"]
 unicode = ["unicodedata2 (>=15.1.0)"]
 woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
+[[package]]
+name = "h11"
+version = "0.14.0"
+description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
 [[package]]
 name = "identify"
-version = "2.5.35"
+version = "2.6.0"
 description = "File identification library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -832,22 +846,22 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "7.1.0"
+version = "8.2.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
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 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
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+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "importlib-resources"
@@ -880,13 +894,13 @@ files = [
 
 [[package]]
 name = "jinja2"
-version = "3.1.3"
+version = "3.1.4"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -897,13 +911,13 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "joblib"
-version = "1.4.0"
+version = "1.4.2"
 description = "Lightweight pipelining with Python functions"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -1019,21 +1033,6 @@ files = [
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 ]
 
-[[package]]
-name = "livereload"
-version = "2.6.3"
-description = "Python LiveReload is an awesome tool for web developers"
-optional = false
-python-versions = "*"
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-[package.dependencies]
-six = "*"
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-
 [[package]]
 name = "markdown-it-py"
 version = "3.0.0"
@@ -1129,13 +1128,13 @@ files = [
 
 [[package]]
 name = "marshmallow"
-version = "3.21.1"
+version = "3.21.3"
 description = "A lightweight library for converting complex datatypes to and from native Python datatypes."
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 [package.extras]
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 tests = ["pytest", "pytz", "simplejson"]
 
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 ]
 
 [package.dependencies]
@@ -1207,13 +1188,16 @@ contourpy = ">=1.0.1"
 cycler = ">=0.10"
 fonttools = ">=4.22.0"
 importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
-kiwisolver = ">=1.0.1"
-numpy = ">=1.20,<2"
+kiwisolver = ">=1.3.1"
+numpy = ">=1.23"
 packaging = ">=20.0"
-pillow = ">=6.2.0"
+pillow = ">=8"
 pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
 
+[package.extras]
+dev = ["meson-python (>=0.13.1)", "numpy (>=1.25)", "pybind11 (>=2.6)", "setuptools (>=64)", "setuptools_scm (>=7)"]
+
 [[package]]
 name = "mccabe"
 version = "0.7.0"
@@ -1261,44 +1245,44 @@ research = ["entsoe-py (>=0.3.2)", "lxml (>=4.6.2)", "python-dotenv (>=0.15.0)",
 
 [[package]]
 name = "mypy"
-version = "1.9.0"
+version = "1.11.0"
 description = "Optional static typing for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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-docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"]
+docs = ["furo", "olefile", "sphinx (>=7.3)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
 fpx = ["olefile"]
 mic = ["olefile"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
@@ -1550,28 +1564,29 @@ xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"
-version = "4.2.0"
-description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "4.2.2"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
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 python-versions = ">=3.8"
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+type = ["mypy (>=1.8)"]
 
 [[package]]
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+version = "1.5.0"
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 python-versions = ">=3.8"
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 ]
 
 [package.extras]
@@ -1580,13 +1595,13 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pre-commit"
-version = "3.5.0"
+version = "3.8.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
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 ]
 
 [package.dependencies]
@@ -1613,13 +1628,13 @@ tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "pycodestyle"
-version = "2.9.1"
+version = "2.12.0"
 description = "Python style guide checker"
 optional = false
-python-versions = ">=3.6"
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 ]
 
 [[package]]
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 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
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-typing-extensions = ">=4.6.1"
+pydantic-core = "2.20.1"
+typing-extensions = {version = ">=4.6.1", markers = "python_version < \"3.13\""}
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
 
 [[package]]
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 [package.dependencies]
@@ -1762,28 +1787,27 @@ toml = ["tomli (>=1.2.3)"]
 
 [[package]]
 name = "pyflakes"
-version = "2.5.0"
+version = "3.2.0"
 description = "passive checker of Python programs"
 optional = false
-python-versions = ">=3.6"
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 files = [
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 ]
 
 [[package]]
 name = "pygments"
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+version = "2.18.0"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 [package.extras]
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 windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
@@ -1802,13 +1826,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
-version = "8.1.1"
+version = "8.3.2"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
@@ -1816,11 +1840,11 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
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 iniconfig = "*"
 packaging = "*"
-pluggy = ">=1.4,<2.0"
+pluggy = ">=1.5,<2"
 tomli = {version = ">=1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
@@ -1867,17 +1891,17 @@ files = [
 
 [[package]]
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+version = "3.17.0"
 description = "A tool to automatically upgrade syntax for newer versions."
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 ]
 
 [package.dependencies]
-tokenize-rt = ">=3.2.0"
+tokenize-rt = ">=5.2.0"
 
 [[package]]
 name = "pyyaml"
@@ -1941,13 +1965,13 @@ files = [
 
 [[package]]
 name = "requests"
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+version = "2.32.3"
 description = "Python HTTP for Humans."
 optional = false
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 pygments = ">=2.13.0,<3.0.0"
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 [package.extras]
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@@ -2071,19 +2094,20 @@ files = [
 
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 python-versions = ">=3.7"
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 [package.dependencies]
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 Click = ">=8.0.2"
 dparse = ">=0.6.4b0"
+filelock = ">=3.12.2,<3.13.0"
 jinja2 = ">=3.1.0"
 marshmallow = ">=3.15.0"
 packaging = ">=21.0"
@@ -2122,104 +2146,106 @@ typing-extensions = ">=4.7.1"
 
 [[package]]
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-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "ordered-set (>=3.1.1)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "shellingham"
@@ -2243,6 +2269,17 @@ files = [
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
 ]
 
+[[package]]
+name = "sniffio"
+version = "1.3.1"
+description = "Sniff out which async library your code is running under"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2"},
+    {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"},
+]
+
 [[package]]
 name = "snowballstemmer"
 version = "2.2.0"
@@ -2256,73 +2293,96 @@ files = [
 
 [[package]]
 name = "sphinx"
-version = "7.1.2"
+version = "7.4.7"
 description = "Python documentation generator"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinx-7.1.2-py3-none-any.whl", hash = "sha256:d170a81825b2fcacb6dfd5a0d7f578a053e45d3f2b153fecc948c37344eb4cbe"},
-    {file = "sphinx-7.1.2.tar.gz", hash = "sha256:780f4d32f1d7d1126576e0e5ecc19dc32ab76cd24e950228dcf7b1f6d3d9e22f"},
+    {file = "sphinx-7.4.7-py3-none-any.whl", hash = "sha256:c2419e2135d11f1951cd994d6eb18a1835bd8fdd8429f9ca375dc1f3281bd239"},
+    {file = "sphinx-7.4.7.tar.gz", hash = "sha256:242f92a7ea7e6c5b406fdc2615413890ba9f699114a9c09192d7dfead2ee9cfe"},
 ]
 
 [package.dependencies]
-alabaster = ">=0.7,<0.8"
-babel = ">=2.9"
-colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.18.1,<0.21"
+alabaster = ">=0.7.14,<0.8.0"
+babel = ">=2.13"
+colorama = {version = ">=0.4.6", markers = "sys_platform == \"win32\""}
+docutils = ">=0.20,<0.22"
 imagesize = ">=1.3"
-importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
-Jinja2 = ">=3.0"
-packaging = ">=21.0"
-Pygments = ">=2.13"
-requests = ">=2.25.0"
-snowballstemmer = ">=2.0"
+importlib-metadata = {version = ">=6.0", markers = "python_version < \"3.10\""}
+Jinja2 = ">=3.1"
+packaging = ">=23.0"
+Pygments = ">=2.17"
+requests = ">=2.30.0"
+snowballstemmer = ">=2.2"
 sphinxcontrib-applehelp = "*"
 sphinxcontrib-devhelp = "*"
 sphinxcontrib-htmlhelp = ">=2.0.0"
 sphinxcontrib-jsmath = "*"
 sphinxcontrib-qthelp = "*"
-sphinxcontrib-serializinghtml = ">=1.1.5"
+sphinxcontrib-serializinghtml = ">=1.1.9"
+tomli = {version = ">=2", markers = "python_version < \"3.11\""}
 
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
-lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-simplify", "isort", "mypy (>=0.990)", "ruff", "sphinx-lint", "types-requests"]
-test = ["cython", "filelock", "html5lib", "pytest (>=4.6)"]
+lint = ["flake8 (>=6.0)", "importlib-metadata (>=6.0)", "mypy (==1.10.1)", "pytest (>=6.0)", "ruff (==0.5.2)", "sphinx-lint (>=0.9)", "tomli (>=2)", "types-docutils (==0.21.0.20240711)", "types-requests (>=2.30.0)"]
+test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools (>=70.0)", "typing_extensions (>=4.9)"]
 
 [[package]]
 name = "sphinx-autobuild"
-version = "2021.3.14"
-description = "Rebuild Sphinx documentation on changes, with live-reload in the browser."
+version = "2024.4.16"
+description = "Rebuild Sphinx documentation on changes, with hot reloading in the browser."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinx-autobuild-2021.3.14.tar.gz", hash = "sha256:de1ca3b66e271d2b5b5140c35034c89e47f263f2cd5db302c9217065f7443f05"},
-    {file = "sphinx_autobuild-2021.3.14-py3-none-any.whl", hash = "sha256:8fe8cbfdb75db04475232f05187c776f46f6e9e04cacf1e49ce81bdac649ccac"},
+    {file = "sphinx_autobuild-2024.4.16-py3-none-any.whl", hash = "sha256:f2522779d30fcbf0253e09714f274ce8c608cb6ebcd67922b1c54de59faba702"},
+    {file = "sphinx_autobuild-2024.4.16.tar.gz", hash = "sha256:1c0ed37a1970eed197f9c5a66d65759e7c4e4cba7b5a5d77940752bf1a59f2c7"},
 ]
 
 [package.dependencies]
 colorama = "*"
-livereload = "*"
 sphinx = "*"
+starlette = ">=0.35"
+uvicorn = ">=0.25"
+watchfiles = ">=0.20"
+websockets = ">=11"
+
+[package.extras]
+test = ["pytest (>=6)"]
+
+[[package]]
+name = "sphinx-autodoc-typehints"
+version = "2.2.3"
+description = "Type hints (PEP 484) support for the Sphinx autodoc extension"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "sphinx_autodoc_typehints-2.2.3-py3-none-any.whl", hash = "sha256:b7058e8c5831e5598afca1a78fda0695d3291388d954464a6e480c36198680c0"},
+    {file = "sphinx_autodoc_typehints-2.2.3.tar.gz", hash = "sha256:fde3d888949bd0a91207cf1e54afda58121dbb4bf1f183d0cc78a0826654c974"},
+]
+
+[package.dependencies]
+sphinx = ">=7.3.5"
 
 [package.extras]
-test = ["pytest", "pytest-cov"]
+docs = ["furo (>=2024.1.29)"]
+numpy = ["nptyping (>=2.5)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.4.4)", "defusedxml (>=0.7.1)", "diff-cover (>=9)", "pytest (>=8.1.1)", "pytest-cov (>=5)", "sphobjinv (>=2.3.1)", "typing-extensions (>=4.11)"]
 
 [[package]]
 name = "sphinx-click"
-version = "5.1.0"
+version = "6.0.0"
 description = "Sphinx extension that automatically documents click applications"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "sphinx-click-5.1.0.tar.gz", hash = "sha256:6812c2db62d3fae71a4addbe5a8a0a16c97eb491f3cd63fe34b4ed7e07236f33"},
-    {file = "sphinx_click-5.1.0-py3-none-any.whl", hash = "sha256:ae97557a4e9ec646045089326c3b90e026c58a45e083b8f35f17d5d6558d08a0"},
+    {file = "sphinx_click-6.0.0-py3-none-any.whl", hash = "sha256:1e0a3c83bcb7c55497751b19d07ebe56b5d7b85eb76dd399cf9061b497adc317"},
+    {file = "sphinx_click-6.0.0.tar.gz", hash = "sha256:f5d664321dc0c6622ff019f1e1c84e58ce0cecfddeb510e004cf60c2a3ab465b"},
 ]
 
 [package.dependencies]
-click = ">=7.0"
+click = ">=8.0"
 docutils = "*"
-sphinx = ">=2.0"
+sphinx = ">=4.0"
 
 [[package]]
 name = "sphinx-rtd-dark-mode"
@@ -2359,47 +2419,50 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
-version = "1.0.4"
+version = "1.0.8"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-applehelp-1.0.4.tar.gz", hash = "sha256:828f867945bbe39817c210a1abfd1bc4895c8b73fcaade56d45357a348a07d7e"},
-    {file = "sphinxcontrib_applehelp-1.0.4-py3-none-any.whl", hash = "sha256:29d341f67fb0f6f586b23ad80e072c8e6ad0b48417db2bde114a4c9746feb228"},
+    {file = "sphinxcontrib_applehelp-1.0.8-py3-none-any.whl", hash = "sha256:cb61eb0ec1b61f349e5cc36b2028e9e7ca765be05e49641c97241274753067b4"},
+    {file = "sphinxcontrib_applehelp-1.0.8.tar.gz", hash = "sha256:c40a4f96f3776c4393d933412053962fac2b84f4c99a7982ba42e09576a70619"},
 ]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
-version = "1.0.2"
-description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
+version = "1.0.6"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
-    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
+    {file = "sphinxcontrib_devhelp-1.0.6-py3-none-any.whl", hash = "sha256:6485d09629944511c893fa11355bda18b742b83a2b181f9a009f7e500595c90f"},
+    {file = "sphinxcontrib_devhelp-1.0.6.tar.gz", hash = "sha256:9893fd3f90506bc4b97bdb977ceb8fbd823989f4316b28c3841ec128544372d3"},
 ]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.1"
+version = "2.0.6"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"},
-    {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"},
+    {file = "sphinxcontrib_htmlhelp-2.0.6-py3-none-any.whl", hash = "sha256:1b9af5a2671a61410a868fce050cab7ca393c218e6205cbc7f590136f207395c"},
+    {file = "sphinxcontrib_htmlhelp-2.0.6.tar.gz", hash = "sha256:c6597da06185f0e3b4dc952777a04200611ef563882e0c244d27a15ee22afa73"},
 ]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["html5lib", "pytest"]
 
 [[package]]
@@ -2432,34 +2495,54 @@ test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
-version = "1.0.3"
-description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
+version = "1.0.8"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
-    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
+    {file = "sphinxcontrib_qthelp-1.0.8-py3-none-any.whl", hash = "sha256:323d6acc4189af76dfe94edd2a27d458902319b60fcca2aeef3b2180c106a75f"},
+    {file = "sphinxcontrib_qthelp-1.0.8.tar.gz", hash = "sha256:db3f8fa10789c7a8e76d173c23364bdf0ebcd9449969a9e6a3dd31b8b7469f03"},
 ]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
+standalone = ["Sphinx (>=5)"]
+test = ["defusedxml (>=0.7.1)", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
-version = "1.1.5"
-description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+version = "1.1.10"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
-    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
+    {file = "sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl", hash = "sha256:326369b8df80a7d2d8d7f99aa5ac577f51ea51556ed974e7716cfd4fca3f6cb7"},
+    {file = "sphinxcontrib_serializinghtml-1.1.10.tar.gz", hash = "sha256:93f3f5dc458b91b192fe10c397e324f262cf163d79f3282c158e8436a2c4511f"},
 ]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
+[[package]]
+name = "starlette"
+version = "0.38.1"
+description = "The little ASGI library that shines."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "starlette-0.38.1-py3-none-any.whl", hash = "sha256:42688a287165bd6acc53068457b5cbf28a3204110b704930411728a633f0f7b8"},
+    {file = "starlette-0.38.1.tar.gz", hash = "sha256:890e89d9b1b367bad6fd11a6e191f40d03504df1ff55fd15674a3b35a122990e"},
+]
+
+[package.dependencies]
+anyio = ">=3.4.0,<5"
+typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""}
+
+[package.extras]
+full = ["httpx (>=0.22.0)", "itsdangerous", "jinja2", "python-multipart (>=0.0.7)", "pyyaml"]
+
 [[package]]
 name = "stevedore"
 version = "5.2.0"
@@ -2476,13 +2559,13 @@ pbr = ">=2.0.0,<2.1.0 || >2.1.0"
 
 [[package]]
 name = "threadpoolctl"
-version = "3.4.0"
+version = "3.5.0"
 description = "threadpoolctl"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "threadpoolctl-3.4.0-py3-none-any.whl", hash = "sha256:8f4c689a65b23e5ed825c8436a92b818aac005e0f3715f6a1664d7c7ee29d262"},
-    {file = "threadpoolctl-3.4.0.tar.gz", hash = "sha256:f11b491a03661d6dd7ef692dd422ab34185d982466c49c8f98c8f716b5c93196"},
+    {file = "threadpoolctl-3.5.0-py3-none-any.whl", hash = "sha256:56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467"},
+    {file = "threadpoolctl-3.5.0.tar.gz", hash = "sha256:082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"},
 ]
 
 [[package]]
@@ -2507,35 +2590,15 @@ files = [
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
 
-[[package]]
-name = "tornado"
-version = "6.4"
-description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
-optional = false
-python-versions = ">= 3.8"
-files = [
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-    {file = "tornado-6.4-cp38-abi3-macosx_10_9_x86_64.whl", hash = "sha256:27787de946a9cffd63ce5814c33f734c627a87072ec7eed71f7fc4417bb16263"},
-    {file = "tornado-6.4-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f7894c581ecdcf91666a0912f18ce5e757213999e183ebfc2c3fdbf4d5bd764e"},
-    {file = "tornado-6.4-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:e43bc2e5370a6a8e413e1e1cd0c91bedc5bd62a74a532371042a18ef19e10579"},
-    {file = "tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f0251554cdd50b4b44362f73ad5ba7126fc5b2c2895cc62b14a1c2d7ea32f212"},
-    {file = "tornado-6.4-cp38-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:fd03192e287fbd0899dd8f81c6fb9cbbc69194d2074b38f384cb6fa72b80e9c2"},
-    {file = "tornado-6.4-cp38-abi3-musllinux_1_1_i686.whl", hash = "sha256:88b84956273fbd73420e6d4b8d5ccbe913c65d31351b4c004ae362eba06e1f78"},
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-    {file = "tornado-6.4-cp38-abi3-win32.whl", hash = "sha256:6f8a6c77900f5ae93d8b4ae1196472d0ccc2775cc1dfdc9e7727889145c45052"},
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-]
-
 [[package]]
 name = "tqdm"
-version = "4.66.2"
+version = "4.66.4"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.2-py3-none-any.whl", hash = "sha256:1ee4f8a893eb9bef51c6e35730cebf234d5d0b6bd112b0271e10ed7c24a02bd9"},
-    {file = "tqdm-4.66.2.tar.gz", hash = "sha256:6cd52cdf0fef0e0f543299cfc96fec90d7b8a7e88745f411ec33eb44d5ed3531"},
+    {file = "tqdm-4.66.4-py3-none-any.whl", hash = "sha256:b75ca56b413b030bc3f00af51fd2c1a1a5eac6a0c1cca83cbb37a5c52abce644"},
+    {file = "tqdm-4.66.4.tar.gz", hash = "sha256:e4d936c9de8727928f3be6079590e97d9abfe8d39a590be678eb5919ffc186bb"},
 ]
 
 [package.dependencies]
@@ -2549,21 +2612,21 @@ telegram = ["requests"]
 
 [[package]]
 name = "typeguard"
-version = "4.2.1"
+version = "4.3.0"
 description = "Run-time type checker for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typeguard-4.2.1-py3-none-any.whl", hash = "sha256:7da3bd46e61f03e0852f8d251dcbdc2a336aa495d7daff01e092b55327796eb8"},
-    {file = "typeguard-4.2.1.tar.gz", hash = "sha256:c556a1b95948230510070ca53fa0341fb0964611bd05d598d87fb52115d65fee"},
+    {file = "typeguard-4.3.0-py3-none-any.whl", hash = "sha256:4d24c5b39a117f8a895b9da7a9b3114f04eb63bade45a4492de49b175b6f7dfa"},
+    {file = "typeguard-4.3.0.tar.gz", hash = "sha256:92ee6a0aec9135181eae6067ebd617fd9de8d75d714fb548728a4933b1dea651"},
 ]
 
 [package.dependencies]
 importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
-typing-extensions = {version = ">=4.10.0", markers = "python_version < \"3.13\""}
+typing-extensions = ">=4.10.0"
 
 [package.extras]
-doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"]
+doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.3.0)"]
 test = ["coverage[toml] (>=7)", "mypy (>=1.2.0)", "pytest (>=7)"]
 
 [[package]]
@@ -2606,13 +2669,13 @@ files = [
 
 [[package]]
 name = "types-requests"
-version = "2.31.0.20240406"
+version = "2.32.0.20240712"
 description = "Typing stubs for requests"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "types-requests-2.31.0.20240406.tar.gz", hash = "sha256:4428df33c5503945c74b3f42e82b181e86ec7b724620419a2966e2de604ce1a1"},
-    {file = "types_requests-2.31.0.20240406-py3-none-any.whl", hash = "sha256:6216cdac377c6b9a040ac1c0404f7284bd13199c0e1bb235f4324627e8898cf5"},
+    {file = "types-requests-2.32.0.20240712.tar.gz", hash = "sha256:90c079ff05e549f6bf50e02e910210b98b8ff1ebdd18e19c873cd237737c1358"},
+    {file = "types_requests-2.32.0.20240712-py3-none-any.whl", hash = "sha256:f754283e152c752e46e70942fa2a146b5bc70393522257bb85bd1ef7e019dcc3"},
 ]
 
 [package.dependencies]
@@ -2620,24 +2683,35 @@ urllib3 = ">=2"
 
 [[package]]
 name = "typing-extensions"
-version = "4.11.0"
+version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"},
+    {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
+    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
+]
+
+[[package]]
+name = "tzdata"
+version = "2024.1"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+files = [
+    {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"},
+    {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "2.2.1"
+version = "2.2.2"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
-    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
+    {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"},
+    {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"},
 ]
 
 [package.extras]
@@ -2646,15 +2720,34 @@ h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
+[[package]]
+name = "uvicorn"
+version = "0.30.3"
+description = "The lightning-fast ASGI server."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "uvicorn-0.30.3-py3-none-any.whl", hash = "sha256:94a3608da0e530cea8f69683aa4126364ac18e3826b6630d1a65f4638aade503"},
+    {file = "uvicorn-0.30.3.tar.gz", hash = "sha256:0d114d0831ff1adbf231d358cbf42f17333413042552a624ea6a9b4c33dcfd81"},
+]
+
+[package.dependencies]
+click = ">=7.0"
+h11 = ">=0.8"
+typing-extensions = {version = ">=4.0", markers = "python_version < \"3.11\""}
+
+[package.extras]
+standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.4)"]
+
 [[package]]
 name = "virtualenv"
-version = "20.25.1"
+version = "20.26.3"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.25.1-py3-none-any.whl", hash = "sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a"},
-    {file = "virtualenv-20.25.1.tar.gz", hash = "sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197"},
+    {file = "virtualenv-20.26.3-py3-none-any.whl", hash = "sha256:8cc4a31139e796e9a7de2cd5cf2489de1217193116a8fd42328f1bd65f434589"},
+    {file = "virtualenv-20.26.3.tar.gz", hash = "sha256:4c43a2a236279d9ea36a0d76f98d84bd6ca94ac4e0f4a3b9d46d05e10fea542a"},
 ]
 
 [package.dependencies]
@@ -2663,18 +2756,186 @@ filelock = ">=3.12.2,<4"
 platformdirs = ">=3.9.1,<5"
 
 [package.extras]
-docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
 test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
+[[package]]
+name = "watchfiles"
+version = "0.22.0"
+description = "Simple, modern and high performance file watching and code reload in python."
+optional = false
+python-versions = ">=3.8"
+files = [
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+    {file = "websockets-12.0-pp38-pypy38_pp73-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c3181df4583c4d3994d31fb235dc681d2aaad744fbdbf94c4802485ececdecf2"},
+    {file = "websockets-12.0-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:b067cb952ce8bf40115f6c19f478dc71c5e719b7fbaa511359795dfd9d1a6468"},
+    {file = "websockets-12.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:00700340c6c7ab788f176d118775202aadea7602c5cc6be6ae127761c16d6b0b"},
+    {file = "websockets-12.0-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e469d01137942849cff40517c97a30a93ae79917752b34029f0ec72df6b46399"},
+    {file = "websockets-12.0-pp39-pypy39_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:ffefa1374cd508d633646d51a8e9277763a9b78ae71324183693959cf94635a7"},
+    {file = "websockets-12.0-pp39-pypy39_pp73-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ba0cab91b3956dfa9f512147860783a1829a8d905ee218a9837c18f683239611"},
+    {file = "websockets-12.0-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:2cb388a5bfb56df4d9a406783b7f9dbefb888c09b71629351cc6b036e9259370"},
+    {file = "websockets-12.0-py3-none-any.whl", hash = "sha256:dc284bbc8d7c78a6c69e0c7325ab46ee5e40bb4d50e494d8131a07ef47500e9e"},
+    {file = "websockets-12.0.tar.gz", hash = "sha256:81df9cbcbb6c260de1e007e58c011bfebe2dafc8435107b0537f393dd38c8b1b"},
+]
+
 [[package]]
 name = "xdoctest"
-version = "1.1.3"
+version = "1.1.5"
 description = "A rewrite of the builtin doctest module"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "xdoctest-1.1.3-py3-none-any.whl", hash = "sha256:9360535bd1a971ffc216d9613898cedceb81d0fd024587cc3c03c74d14c00a31"},
-    {file = "xdoctest-1.1.3.tar.gz", hash = "sha256:84e76a42a11a5926ff66d9d84c616bc101821099672550481ad96549cbdd02ae"},
+    {file = "xdoctest-1.1.5-py3-none-any.whl", hash = "sha256:f36fe64d7c0ad0553dbff39ff05c43a0aab69d313466f24a38d00e757182ade0"},
+    {file = "xdoctest-1.1.5.tar.gz", hash = "sha256:89b0c3ad7fe03a068e22a457ab18c38fc70c62329c2963f43954b83c29374e66"},
 ]
 
 [package.dependencies]
@@ -2695,20 +2956,20 @@ tests-strict = ["pytest (==4.6.0)", "pytest (==4.6.0)", "pytest (==6.2.5)", "pyt
 
 [[package]]
 name = "zipp"
-version = "3.18.1"
+version = "3.19.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
-    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
+    {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
+    {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = ">=3.8.0,<3.11.0"
-content-hash = "d200011cd83d83ad3e0a834c204c8b1e20f45505d64ad420b5478b81482fcbf7"
+python-versions = ">=3.9.0,<3.11.0"
+content-hash = "f11f8a0e0b033de143e785dc13fa807e13065325e1619013150804d9a232c4b1"
diff --git a/pyproject.toml b/pyproject.toml
index 077ef18..9bebb9a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,31 +1,29 @@
 [tool.poetry]
 name = "spectrum_fundamentals"
-version = "0.5.2"  # <<COOKIETEMPLE_FORCE_BUMP>>
+version = "0.7.8"  # <<COOKIETEMPLE_FORCE_BUMP>>
 description = "Fundamental functions, annotation pipeline and constants for oktoberfest"
 authors = ["Wilhelmlab at Technical University of Munich"]
 license = "MIT"
 readme = "README.rst"
 homepage = "https://github.com/wilhelm-lab/spectrum_fundamentals"
 repository = "https://github.com/wilhelm-lab/spectrum_fundamentals"
-documentation = "https://spectrum_fundamentals.readthedocs.io"
+documentation = "https://spectrum-fundamentals.readthedocs.io"
 packages = [
     { include = "spectrum_fundamentals" },
 ]
 classifiers = [
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
 ]
 
 
 [tool.poetry.dependencies]
-python = ">=3.8.0,<3.11.0"
+python = ">=3.9.0,<3.11.0"
 click = ">=8.0.0"
 rich = ">=10.3.0"
 PyYAML = ">=5.4.1"
 numpy = ">=1.24.1,<1.25"
-pandas = "^1.3.0"
+pandas = ">=1.3,<3.0"
 scikit-learn = "^1.0"
 joblib = "^1.0.1"
 moepy = "^1.1.4"
@@ -63,6 +61,9 @@ pyupgrade = ">=2.31.0"
 [tool.poetry.scripts]
 spectrum_fundamentals = "spectrum_fundamentals.__main__:main"
 
+[tool.poetry.group.dev.dependencies]
+sphinx-autodoc-typehints = "^2.2.3"
+
 [tool.black]
 line-length = 120
 
diff --git a/requirements.txt b/requirements.txt
index 6c22d04..5c606cc 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,29 +1,122 @@
-click==8.1.7 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-colorama==0.4.6 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" and platform_system == "Windows"
-contourpy==1.1.1 ; python_version >= "3.8" and python_full_version < "3.11.0"
-cycler==0.12.1 ; python_version >= "3.8" and python_full_version < "3.11.0"
-fonttools==4.51.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.10"
-joblib==1.4.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-kiwisolver==1.4.5 ; python_version >= "3.8" and python_full_version < "3.11.0"
-markdown-it-py==3.0.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-matplotlib==3.7.5 ; python_version >= "3.8" and python_full_version < "3.11.0"
-mdurl==0.1.2 ; python_version >= "3.8" and python_full_version < "3.11.0"
-moepy==1.1.4 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-numpy==1.24.4 ; python_version >= "3.8" and python_full_version < "3.11.0"
-packaging==24.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-pandas==1.5.3 ; python_version >= "3.8" and python_full_version < "3.11.0"
-pillow==10.3.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-pygments==2.17.2 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-pyparsing==3.1.2 ; python_version >= "3.8" and python_full_version < "3.11.0"
-python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-pytz==2024.1 ; python_version >= "3.8" and python_full_version < "3.11.0"
-pyyaml==6.0.1 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-rich==13.7.1 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-scikit-learn==1.3.2 ; python_version >= "3.8" and python_full_version < "3.11.0"
-scipy==1.10.1 ; python_version >= "3.8" and python_full_version < "3.11.0"
-six==1.16.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-threadpoolctl==3.4.0 ; python_version >= "3.8" and python_full_version < "3.11.0"
-tqdm==4.66.2 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0"
-typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.9"
-zipp==3.18.1 ; python_version >= "3.8" and python_version < "3.10"
+alabaster==0.7.16 ; python_version >= "3.9" and python_full_version < "3.11.0"
+annotated-types==0.7.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+anyio==4.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+attrs==23.2.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+authlib==1.3.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+babel==2.15.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+bandit==1.7.9 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+black==24.4.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+certifi==2024.7.4 ; python_version >= "3.9" and python_full_version < "3.11.0"
+cffi==1.16.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" and platform_python_implementation != "PyPy"
+cfgv==3.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+charset-normalizer==3.3.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+click==8.1.7 ; python_version >= "3.9" and python_full_version < "3.11.0"
+colorama==0.4.6 ; python_version >= "3.9" and python_full_version < "3.11.0"
+contourpy==1.2.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+coverage[toml]==7.6.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+cryptography==43.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+cycler==0.12.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+darglint==1.8.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+distlib==0.3.8 ; python_version >= "3.9" and python_full_version < "3.11.0"
+docutils==0.20.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+dparse==0.6.4b0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+exceptiongroup==1.2.2 ; python_version >= "3.9" and python_version < "3.11"
+filelock==3.12.4 ; python_version >= "3.9" and python_full_version < "3.11.0"
+flake8-bandit==4.1.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+flake8-bugbear==24.4.26 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+flake8-docstrings==1.7.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+flake8-rst-docstrings==0.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+flake8==7.1.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+fonttools==4.53.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+h11==0.14.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+identify==2.6.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+idna==3.7 ; python_version >= "3.9" and python_full_version < "3.11.0"
+imagesize==1.4.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+importlib-metadata==8.2.0 ; python_version >= "3.9" and python_version < "3.10"
+importlib-resources==6.4.0 ; python_version >= "3.9" and python_version < "3.10"
+iniconfig==2.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+jinja2==3.1.4 ; python_version >= "3.9" and python_full_version < "3.11.0"
+joblib==1.4.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+kiwisolver==1.4.5 ; python_version >= "3.9" and python_full_version < "3.11.0"
+markdown-it-py==3.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+markupsafe==2.1.5 ; python_version >= "3.9" and python_full_version < "3.11.0"
+marshmallow==3.21.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+matplotlib==3.9.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+mccabe==0.7.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+mdurl==0.1.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+moepy==1.1.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+mypy-extensions==1.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+mypy==1.11.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+nodeenv==1.9.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+numpy==1.24.4 ; python_version >= "3.9" and python_version < "3.11"
+packaging==24.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pandas==2.2.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pathspec==0.12.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pbr==6.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pep8-naming==0.14.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pillow==10.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+platformdirs==4.2.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pluggy==1.5.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pre-commit-hooks==4.6.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pre-commit==3.8.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pycodestyle==2.12.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pycparser==2.22 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" and platform_python_implementation != "PyPy"
+pydantic-core==2.20.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pydantic==2.8.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pydocstyle==6.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pyflakes==3.2.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pygments==2.18.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pyparsing==3.1.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pytest-cov==5.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+pytest==8.3.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pytz==2024.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pyupgrade==3.17.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+pyyaml==6.0.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+requests==2.32.3 ; python_version >= "3.9" and python_full_version < "3.11.0"
+restructuredtext-lint==1.4.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+rich==13.7.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_full_version < "3.11.0" and python_full_version >= "3.9.0"
+ruamel-yaml==0.18.6 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+safety-schemas==0.0.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+safety==3.2.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+scikit-learn==1.5.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+scipy==1.13.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+setuptools==71.1.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+shellingham==1.5.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+six==1.16.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+sniffio==1.3.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+snowballstemmer==2.2.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+sphinx-autobuild==2024.4.16 ; python_version >= "3.9" and python_full_version < "3.11.0"
+sphinx-autodoc-typehints==2.2.3 ; python_version >= "3.9" and python_full_version < "3.11.0"
+sphinx-click==6.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+sphinx-rtd-dark-mode==1.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+sphinx-rtd-theme==2.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+sphinx==7.4.7 ; python_version >= "3.9" and python_full_version < "3.11.0"
+sphinxcontrib-applehelp==1.0.8 ; python_version >= "3.9" and python_full_version < "3.11.0"
+sphinxcontrib-devhelp==1.0.6 ; python_version >= "3.9" and python_full_version < "3.11.0"
+sphinxcontrib-htmlhelp==2.0.6 ; python_version >= "3.9" and python_full_version < "3.11.0"
+sphinxcontrib-jquery==4.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+sphinxcontrib-qthelp==1.0.8 ; python_version >= "3.9" and python_full_version < "3.11.0"
+sphinxcontrib-serializinghtml==1.1.10 ; python_version >= "3.9" and python_full_version < "3.11.0"
+starlette==0.38.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+stevedore==5.2.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+threadpoolctl==3.5.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+tokenize-rt==5.2.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+tomli==2.0.1 ; python_version >= "3.9" and python_version < "3.11"
+tqdm==4.66.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+typeguard==4.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+typer==0.12.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+types-attrs==19.1.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+types-pkg-resources==0.1.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+types-requests==2.32.0.20240712 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+typing-extensions==4.12.2 ; python_version >= "3.9" and python_version < "3.11"
+tzdata==2024.1 ; python_version >= "3.9" and python_full_version < "3.11.0"
+urllib3==2.2.2 ; python_version >= "3.9" and python_full_version < "3.11.0"
+uvicorn==0.30.3 ; python_version >= "3.9" and python_full_version < "3.11.0"
+virtualenv==20.26.3 ; python_version >= "3.9" and python_full_version < "3.11.0"
+watchfiles==0.22.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+websockets==12.0 ; python_version >= "3.9" and python_full_version < "3.11.0"
+xdoctest[colors]==1.1.5 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0"
+zipp==3.19.2 ; python_version >= "3.9" and python_version < "3.10"
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 137edab..0000000
--- a/setup.py
+++ /dev/null
@@ -1,28 +0,0 @@
-from setuptools import setup
-
-packages = ["fundamentals", "fundamentals.annotation", "fundamentals.metrics"]
-
-package_data = {"": ["*"]}
-
-install_requires = ["numpy>=1.21.0,<2.0.0", "pandas>=1.3.0,<2.0.0", "statsmodels>=0.12.2,<0.13.0"]
-
-setup_kwargs = {
-    "name": "fundamentals",
-    "version": "0.1.0",
-    "description": "",
-    "long_description": None,
-    "author": "WassimG",
-    "author_email": "wassim.gabriel@gmail.com",
-    "maintainer": None,
-    "maintainer_email": None,
-    "url": None,
-    "packages": packages,
-    "package_data": package_data,
-    "install_requires": install_requires,
-    "python_requires": ">=3.8,<4.0",
-}
-
-
-setup(**setup_kwargs)
-
-# This setup.py was autogenerated using poetry.
diff --git a/spectrum_fundamentals/__init__.py b/spectrum_fundamentals/__init__.py
index 413d645..741dd90 100644
--- a/spectrum_fundamentals/__init__.py
+++ b/spectrum_fundamentals/__init__.py
@@ -1,8 +1,11 @@
-"""Initialize fundamentals."""
+"""Spectrum Fundamentals."""
 
-__author__ = "Mario Picciani"
-__email__ = "mario.picciani@tum.de"
-__version__ = "0.5.2"
+from datetime import datetime
+
+__author__ = """The Oktoberfest development team (Wilhelmlab at Technical University of Munich)"""
+__copyright__ = f"Copyright {datetime.now():%Y}, Wilhelmlab at Technical University of Munich"
+__license__ = "MIT"
+__version__ = "0.7.8"
 
 import logging
 import logging.handlers
diff --git a/spectrum_fundamentals/__main__.py b/spectrum_fundamentals/__main__.py
index 75c0534..e59a495 100644
--- a/spectrum_fundamentals/__main__.py
+++ b/spectrum_fundamentals/__main__.py
@@ -5,7 +5,7 @@
 
 
 @click.command()
-@click.version_option(version="0.5.2", message=click.style("spectrum_fundamentals Version: 0.5.2"))
+@click.version_option(version="0.7.8", message=click.style("spectrum_fundamentals Version: 0.7.8"))
 def main() -> None:
     """spectrum_fundamentals."""
 
diff --git a/spectrum_fundamentals/annotation/annotation.py b/spectrum_fundamentals/annotation/annotation.py
index 98dbd81..90d3f3b 100644
--- a/spectrum_fundamentals/annotation/annotation.py
+++ b/spectrum_fundamentals/annotation/annotation.py
@@ -5,7 +5,7 @@
 import pandas as pd
 
 from spectrum_fundamentals import constants
-from spectrum_fundamentals.fragments import initialize_peaks, initialize_peaks_xl
+from spectrum_fundamentals.fragments import initialize_peaks, initialize_peaks_xl, retrieve_ion_types
 
 logger = logging.getLogger(__name__)
 
@@ -17,7 +17,7 @@ def match_peaks(
     tmt_n_term: int,
     unmod_sequence: str,
     charge: int,
-) -> List[Dict[str, Union[str, int, float]]]:
+) -> Tuple[List[Dict[str, Union[str, int, float]]], int]:
     """
     Matching experimental peaks with theoretical fragment ions.
 
@@ -31,12 +31,12 @@ def match_peaks(
     """
     start_peak = 0
     no_of_peaks = len(peaks_intensity)
-    max_intensity = 1.0
+    max_intensity = 0.0
     row_list = []
     temp_list = []
     next_start_peak = 0
-    seq_len = len(unmod_sequence)
     matched_peak = False
+    count_annotated_nl = 0
     fragment_no: float
     for fragment in fragments_meta_data:
         min_mass = fragment["min_mass"]
@@ -55,29 +55,34 @@ def match_peaks(
                 start_peak += 1
                 continue
             if (
-                not (fragment["ion_type"] == "b" and fragment_no == 1)
+                not (fragment["ion_type"][0] == "b" and fragment_no == 1)
                 or (unmod_sequence[0] == "R" or unmod_sequence[0] == "H" or unmod_sequence[0] == "K")
-                and (tmt_n_term == 1)
+                or (tmt_n_term == 2)
             ):
-                row_list.append(
-                    {
-                        "ion_type": fragment["ion_type"],
-                        "no": fragment_no,
-                        "charge": fragment["charge"],
-                        "exp_mass": peak_mass,
-                        "theoretical_mass": fragment["mass"],
-                        "intensity": peak_intensity,
-                    }
-                )
-                if peak_intensity > max_intensity and fragment_no < seq_len:
-                    max_intensity = float(peak_intensity)
+                # For now only counting neutral loss peaks this can change with different models later
+                if fragment["neutral_loss"] == "":
+                    row_list.append(
+                        {
+                            "ion_type": fragment["ion_type"],
+                            "no": fragment_no,
+                            "charge": fragment["charge"],
+                            "exp_mass": peak_mass,
+                            "theoretical_mass": fragment["mass"],
+                            "intensity": peak_intensity,
+                        }
+                    )
+                    if peak_intensity > max_intensity:
+                        max_intensity = float(peak_intensity)
+                else:
+                    count_annotated_nl += 1
+
             matched_peak = True
             next_start_peak = start_peak
             start_peak += 1
     for row in row_list:
         row["intensity"] = float(row["intensity"]) / max_intensity
         temp_list.append(row)
-    return temp_list
+    return temp_list, count_annotated_nl
 
 
 def handle_multiple_matches(
@@ -119,7 +124,12 @@ def handle_multiple_matches(
 
 
 def annotate_spectra(
-    un_annot_spectra: pd.DataFrame, mass_tolerance: Optional[float] = None, unit_mass_tolerance: Optional[str] = None
+    un_annot_spectra: pd.DataFrame,
+    mass_tolerance: Optional[float] = None,
+    unit_mass_tolerance: Optional[str] = None,
+    custom_mods: Optional[Dict[str, float]] = None,
+    fragmentation_method: str = "HCD",
+    annotate_neutral_loss: Optional[bool] = False,
 ) -> pd.DataFrame:
     """
     Annotate a set of spectra.
@@ -138,19 +148,37 @@ def annotate_spectra(
     :param un_annot_spectra: a Pandas DataFrame containing the raw peaks and metadata to be annotated
     :param mass_tolerance: mass tolerance to calculate min and max mass
     :param unit_mass_tolerance: unit for the mass tolerance (da or ppm)
+    :param fragmentation_method: fragmentation method that was used
+    :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
+    :param annotate_neutral_loss: flag to indicate whether to annotate neutral losses or not
     :return: a Pandas DataFrame containing the annotated spectra with meta data
     """
     raw_file_annotations = []
     index_columns = {col: un_annot_spectra.columns.get_loc(col) for col in un_annot_spectra.columns}
     for row in un_annot_spectra.values:
-        results = parallel_annotate(row, index_columns, mass_tolerance, unit_mass_tolerance)
+        results = parallel_annotate(
+            row,
+            index_columns,
+            mass_tolerance,
+            unit_mass_tolerance,
+            fragmentation_method=fragmentation_method,
+            custom_mods=custom_mods,
+            annotate_neutral_losses=annotate_neutral_loss,
+        )
         if not results:
             continue
         raw_file_annotations.append(results)
     results_df = pd.DataFrame(raw_file_annotations)
 
     if "CROSSLINKER_TYPE" not in index_columns:
-        results_df.columns = ["INTENSITIES", "MZ", "CALCULATED_MASS", "removed_peaks"]
+        results_df.columns = [
+            "INTENSITIES",
+            "MZ",
+            "CALCULATED_MASS",
+            "removed_peaks",
+            "ANNOTATED_NL_COUNT",
+            "EXPECTED_NL_COUNT",
+        ]
     else:
         results_df.columns = [
             "INTENSITIES_A",
@@ -269,7 +297,7 @@ def generate_annotation_matrix_xl(
 
 
 def generate_annotation_matrix(
-    matched_peaks: pd.DataFrame, unmod_seq: str, charge: int
+    matched_peaks: pd.DataFrame, unmod_seq: str, charge: int, fragmentation_method: str = "HCD"
 ) -> Tuple[np.ndarray, np.ndarray]:
     """
     Generate the annotation matrix in the prosit format from matched peaks.
@@ -277,16 +305,21 @@ def generate_annotation_matrix(
     :param matched_peaks: matched peaks needed to be converted
     :param unmod_seq: Un modified peptide sequence
     :param charge: Precursor charge
+    :param fragmentation_method: fragmentation method that was used
     :return: numpy array of intensities and numpy array of masses
     """
-    intensity = np.full(constants.VEC_LENGTH, -1.0)
-    mass = np.full(constants.VEC_LENGTH, -1.0)
+    ion_types = retrieve_ion_types(fragmentation_method)
+    charge_const = 3
+    vec_length = (constants.SEQ_LEN - 1) * charge_const * len(ion_types)
+
+    intensity = np.full(vec_length, -1.0)
+    mass = np.full(vec_length, -1.0)
 
     # change values to zeros
     if len(unmod_seq) < constants.SEQ_LEN:
-        peaks_range = range(0, ((len(unmod_seq) - 1) * 6))
+        peaks_range = range(0, ((len(unmod_seq) - 1) * charge_const * len(ion_types)))
     else:
-        peaks_range = range(0, ((constants.SEQ_LEN - 1) * 6))
+        peaks_range = range(0, ((constants.SEQ_LEN - 1) * charge_const * len(ion_types)))
 
     if charge == 1:
         available_peaks = [index for index in peaks_range if (index % 3 == 0)]
@@ -305,10 +338,8 @@ def generate_annotation_matrix(
     exp_mass_col = matched_peaks.columns.get_loc("exp_mass")
 
     for peak in matched_peaks.values:
-        if peak[ion_type].startswith("y"):
-            peak_pos = ((peak[no_col] - 1) * 6) + (peak[charge_col] - 1)
-        else:
-            peak_pos = ((peak[no_col] - 1) * 6) + (peak[charge_col] - 1) + 3
+        ion_type_index = ion_types.index(peak[ion_type].split("-", 1)[0])
+        peak_pos = ((peak[no_col] - 1) * charge_const * len(ion_types)) + (peak[charge_col] - 1) + 3 * ion_type_index
 
         if peak_pos >= constants.VEC_LENGTH:
             continue
@@ -316,7 +347,9 @@ def generate_annotation_matrix(
         mass[peak_pos] = peak[exp_mass_col]
 
     if len(unmod_seq) < constants.SEQ_LEN:
-        mask_peaks = range((len(unmod_seq) - 1) * 6, ((len(unmod_seq) - 1) * 6) + 6)
+        mask_peaks = range(
+            (len(unmod_seq) - 1) * charge_const * len(ion_types), ((len(unmod_seq)) * charge_const * len(ion_types))
+        )
         intensity[mask_peaks] = -1.0
         mass[mask_peaks] = -1.0
 
@@ -328,9 +361,12 @@ def parallel_annotate(
     index_columns: Dict[str, int],
     mass_tolerance: Optional[float] = None,
     unit_mass_tolerance: Optional[str] = None,
+    custom_mods: Optional[Dict[str, float]] = None,
+    fragmentation_method: str = "HCD",
+    annotate_neutral_losses: Optional[bool] = False,
 ) -> Optional[
     Union[
-        Tuple[np.ndarray, np.ndarray, float, int],
+        Tuple[np.ndarray, np.ndarray, float, int, int, int],
         Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, float, float, int, int],
     ]
 ]:
@@ -348,6 +384,9 @@ def parallel_annotate(
     :param index_columns: a dictionary that contains the index columns of the spectrum
     :param mass_tolerance: mass tolerance to calculate min and max mass
     :param unit_mass_tolerance: unit for the mass tolerance (da or ppm)
+    :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
+    :param fragmentation_method: fragmentation method that was used
+    :param annotate_neutral_losses: flag to indicate whether to annotate neutral losses or not
     :return: a tuple containing intensity values (np.ndarray), masses (np.ndarray), calculated mass (float),
              and any removed peaks (List[str])
     """
@@ -355,12 +394,20 @@ def parallel_annotate(
     if xl_type_col is None:
         if spectrum[index_columns["PEPTIDE_LENGTH"]] > 30:  # this was in initialize peaks but can be checked prior
             return None
-        return _annotate_linear_spectrum(spectrum, index_columns, mass_tolerance, unit_mass_tolerance)
+        return _annotate_linear_spectrum(
+            spectrum,
+            index_columns,
+            mass_tolerance,
+            unit_mass_tolerance,
+            fragmentation_method=fragmentation_method,
+            custom_mods=custom_mods,
+            add_neutral_losses=annotate_neutral_losses,
+        )
 
     if (spectrum[index_columns["PEPTIDE_LENGTH_A"]] > 30) or (spectrum[index_columns["PEPTIDE_LENGTH_B"]] > 30):
         return None
     return _annotate_crosslinked_spectrum(
-        spectrum, index_columns, spectrum[xl_type_col], mass_tolerance, unit_mass_tolerance
+        spectrum, index_columns, spectrum[xl_type_col], mass_tolerance, unit_mass_tolerance, custom_mods=custom_mods
     )
 
 
@@ -369,6 +416,9 @@ def _annotate_linear_spectrum(
     index_columns: Dict[str, int],
     mass_tolerance: Optional[float],
     unit_mass_tolerance: Optional[str],
+    custom_mods: Optional[Dict[str, float]] = None,
+    fragmentation_method: str = "HCD",
+    add_neutral_losses: Optional[bool] = False,
 ):
     """
     Annotate a linear peptide spectrum.
@@ -377,19 +427,26 @@ def _annotate_linear_spectrum(
     :param index_columns: Index columns of the spectrum
     :param mass_tolerance: Mass tolerance for calculating min and max mass
     :param unit_mass_tolerance: Unit for the mass tolerance (da or ppm)
+    :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
+    :param fragmentation_method: fragmentation method that was used
+    :param add_neutral_losses: flag to indicate whether to annotate neutral losses or not
     :return: Annotated spectrum
     """
     mod_seq_column = "MODIFIED_SEQUENCE"
     if "MODIFIED_SEQUENCE_MSA" in index_columns:
         mod_seq_column = "MODIFIED_SEQUENCE_MSA"
-    fragments_meta_data, tmt_n_term, unmod_sequence, calc_mass = initialize_peaks(
-        spectrum[index_columns[mod_seq_column]],
-        spectrum[index_columns["MASS_ANALYZER"]],
-        spectrum[index_columns["PRECURSOR_CHARGE"]],
-        mass_tolerance,
-        unit_mass_tolerance,
+
+    fragments_meta_data, tmt_n_term, unmod_sequence, calc_mass, expected_nl = initialize_peaks(
+        sequence=spectrum[index_columns[mod_seq_column]],
+        mass_analyzer=spectrum[index_columns["MASS_ANALYZER"]],
+        charge=spectrum[index_columns["PRECURSOR_CHARGE"]],
+        mass_tolerance=mass_tolerance,
+        unit_mass_tolerance=unit_mass_tolerance,
+        fragmentation_method=fragmentation_method,
+        custom_mods=custom_mods,
+        add_neutral_losses=add_neutral_losses,
     )
-    matched_peaks = match_peaks(
+    matched_peaks, count_annotated_nl = match_peaks(
         fragments_meta_data,
         spectrum[index_columns["INTENSITIES"]],
         spectrum[index_columns["MZ"]],
@@ -398,16 +455,20 @@ def _annotate_linear_spectrum(
         spectrum[index_columns["PRECURSOR_CHARGE"]],
     )
 
+    ion_types = retrieve_ion_types(fragmentation_method)
+    charge_const = 3
+    vec_length = (constants.SEQ_LEN - 1) * charge_const * len(ion_types)
+
     if len(matched_peaks) == 0:
-        intensity = np.full(174, 0.0)
-        mass = np.full(174, 0.0)
-        return intensity, mass, calc_mass, 0
+        intensity = np.full(vec_length, 0.0)
+        mass = np.full(vec_length, 0.0)
+        return intensity, mass, calc_mass, 0, 0, 0
 
     matched_peaks, removed_peaks = handle_multiple_matches(matched_peaks)
     intensities, mass = generate_annotation_matrix(
-        matched_peaks, unmod_sequence, spectrum[index_columns["PRECURSOR_CHARGE"]]
+        matched_peaks, unmod_sequence, spectrum[index_columns["PRECURSOR_CHARGE"]], fragmentation_method
     )
-    return intensities, mass, calc_mass, removed_peaks
+    return intensities, mass, calc_mass, removed_peaks, count_annotated_nl, expected_nl
 
 
 def _annotate_crosslinked_spectrum(
@@ -416,6 +477,7 @@ def _annotate_crosslinked_spectrum(
     crosslinker_type: str,
     mass_tolerance: Optional[float] = None,
     unit_mass_tolerance: Optional[str] = None,
+    custom_mods: Optional[Dict[str, float]] = None,
 ):
     """
     Annotate a crosslinked peptide spectrum.
@@ -425,6 +487,7 @@ def _annotate_crosslinked_spectrum(
     :param crosslinker_type: Type of crosslinker used
     :param mass_tolerance: Mass tolerance for calculating min and max mass
     :param unit_mass_tolerance: Unit for the mass tolerance (da or ppm)
+    :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
     :raises ValueError: if unsupported crosslinker type was supplied.
 
     :return: Annotated spectrum
@@ -451,8 +514,9 @@ def _xl_annotation_workflow(seq_id: str, non_cl_xl: bool):
 
         else:
             array_size = 348
+        inputs.append(custom_mods)
         fragments_meta_data, tmt_n_term, unmod_sequence, calc_mass = initialize_peaks_xl(*inputs)
-        matched_peaks = match_peaks(
+        matched_peaks, annotated_nl = match_peaks(
             fragments_meta_data,
             np.array(spectrum[index_columns["INTENSITIES"]]),
             np.array(spectrum[index_columns["MZ"]]),  # Convert to numpy array
diff --git a/spectrum_fundamentals/constants.py b/spectrum_fundamentals/constants.py
index 1ed7fa2..35d7bba 100644
--- a/spectrum_fundamentals/constants.py
+++ b/spectrum_fundamentals/constants.py
@@ -17,6 +17,8 @@
 VEC_LENGTH_CMS2 = (SEQ_LEN - 1) * 2 * 3 * 2
 # peptide of length 30 can have 29 b, y, b_short, y_short, b_long and y_long ions, each with charge 1+, 2+ and 3+
 # we do not annotate fragments wth charge 3+. All fragmets with charge 3+ convert to -1
+
+
 #############
 # ALPHABETS #
 #############
@@ -113,6 +115,9 @@
     "K[230]": "K[UNIMOD:737]",
     "K[305]": "K[UNIMOD:2016]",
     "K[214]": "K[UNIMOD:214]",
+    "R[157]": "R[UNIMOD:7]",
+    "Q[129]": "Q[UNIMOD:7]",
+    "N[115]": "N[UNIMOD:7]",
     "n[230]": "[UNIMOD:737]-",
     "n[305]": "[UNIMOD:2016]-",
     "n[214]": "[UNIMOD:214]-",
@@ -146,12 +151,7 @@
 PARTICLE_MASSES = {"PROTON": 1.007276467, "ELECTRON": 0.00054858}
 
 # masses of different atoms
-ATOM_MASSES = {
-    "H": 1.007825035,
-    "C": 12.0,
-    "O": 15.9949146,
-    "N": 14.003074,
-}
+ATOM_MASSES = {"H": 1.007825035, "C": 12.0, "O": 15.9949146, "N": 14.003074, "S": 31.9720712, "P": 30.9737619}
 
 MASSES = {**PARTICLE_MASSES, **ATOM_MASSES}
 MASSES["N_TERMINUS"] = MASSES["H"]
@@ -242,20 +242,24 @@
     "[UNIMOD:747]": 86.000394,  # Malonylation
 }
 
+
 MOD_MASSES_SAGE = {
-    229.1629: "[UNIMOD:737]",
-    304.2071: "[UNIMOD:2016]",
-    144.1020: "[UNIMOD:214]",
-    304.2053: "[UNIMOD:730]",
-    8.0141: "[UNIMOD:259]",
-    10.0082: "[UNIMOD:267]",
-    79.9663: "[UNIMOD:21]",
-    -18.0105: "[UNIMOD:23]",
-    57.0214: "[UNIMOD:4]",
-    15.9949: "[UNIMOD:35]",
-    42.0105: "[UNIMOD:1]",
+    "229.1629": "[UNIMOD:737]",
+    "304.2071": "[UNIMOD:2016]",
+    "144.1020": "[UNIMOD:214]",
+    "304.2053": "[UNIMOD:730]",
+    "8.0141": "[UNIMOD:259]",
+    "10.0082": "[UNIMOD:267]",
+    "79.9663": "[UNIMOD:21]",
+    "-18.0105": "[UNIMOD:23]",
+    "57.0215": "[UNIMOD:4]",
+    "15.9949": "[UNIMOD:35]",
+    "15.994": "[UNIMOD:35]",
+    "42.0105": "[UNIMOD:1]",
 }
 # these are only used for prosit_grpc, oktoberfest uses the masses from MOD_MASSES
+
+
 AA_MOD_MASSES = {
     "K[UNIMOD:737]": AA_MASSES["K"] + MOD_MASSES["[UNIMOD:737]"],
     "M[UNIMOD:35]": AA_MASSES["M"] + MOD_MASSES["[UNIMOD:35]"],
@@ -286,6 +290,62 @@
 
 AA_MOD = {**AA_MASSES, **AA_MOD_MASSES}
 
+
+AA_Neutral_losses = {
+    "R": ["NH3", "CH2N2", "C3H9N3"],
+    "N": ["NH3", "CH3NO", "C2H5NO", "C3H5NO"],
+    "D": ["H2O", "CO2", "C2H4O2"],
+    "C": ["CH2S"],
+    "E": ["H2O", "C2H4O2"],
+    "Q": ["NH3", "CH3NO", "C2H5NO", "C3H5NO"],
+    "I": ["C2H4"],
+    "L": ["C3H6", "C4H8"],
+    "K": ["C2H5N", "C4H9N", "C4H11N", "C3H9N"],
+    "M": ["C2H4S", "C3H6S"],
+    "M[UNIMOD:35]": ["CH4SO", "C3H8SO", "C3H6SO"],
+    "S": ["H2O", "CH4O"],
+    "T": ["H2O", "C2H4O"],
+    "W": ["C8H7N", "C9H9N"],
+    "V": ["C3H6"],
+    "[]-": ["NH3"],
+    "-[]": ["H2O"],
+}
+
+Mod_Neutral_losses = {"R[UNIMOD:7]": ["CHNO"], "S[UNIMOD:21]": ["H3O4P"]}
+
+Neutral_losses_Mass = {
+    "C2H4": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 4),
+    "C2H4O": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 4) + ATOM_MASSES["O"],
+    "C2H4O2": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 4) + (ATOM_MASSES["O"] * 2),
+    "C2H4S": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 4) + ATOM_MASSES["S"],
+    "C2H5N": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 5) + ATOM_MASSES["N"],
+    "CHNO": (ATOM_MASSES["C"]) + (ATOM_MASSES["H"]) + ATOM_MASSES["N"] + ATOM_MASSES["O"],
+    "C2H5NO": (ATOM_MASSES["C"] * 2) + (ATOM_MASSES["H"] * 5) + ATOM_MASSES["N"] + ATOM_MASSES["O"],
+    "C3H5NO": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 5) + ATOM_MASSES["N"] + ATOM_MASSES["O"],
+    "C3H6": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 6),
+    "C3H6S": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 6) + ATOM_MASSES["S"],
+    "C3H6SO": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 6) + ATOM_MASSES["S"] + ATOM_MASSES["O"],
+    "C3H8SO": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 8) + ATOM_MASSES["S"] + ATOM_MASSES["O"],
+    "C3H9N": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 9) + ATOM_MASSES["N"],
+    "C3H9N3": (ATOM_MASSES["C"] * 3) + (ATOM_MASSES["H"] * 9) + (ATOM_MASSES["N"] * 3),
+    "C4H11N": (ATOM_MASSES["C"] * 4) + (ATOM_MASSES["H"] * 11) + ATOM_MASSES["N"],
+    "C4H8": (ATOM_MASSES["C"] * 4) + (ATOM_MASSES["H"] * 8),
+    "C4H9N": (ATOM_MASSES["C"] * 4) + (ATOM_MASSES["H"] * 9) + ATOM_MASSES["N"],
+    "C8H7N": (ATOM_MASSES["C"] * 8) + (ATOM_MASSES["H"] * 7) + ATOM_MASSES["N"],
+    "C9H9N": (ATOM_MASSES["C"] * 9) + (ATOM_MASSES["H"] * 9) + ATOM_MASSES["N"],
+    "CH2N2": ATOM_MASSES["C"] + (ATOM_MASSES["H"] * 2) + (ATOM_MASSES["N"] * 2),
+    "CH2S": ATOM_MASSES["C"] + (ATOM_MASSES["H"] * 2) + ATOM_MASSES["S"],
+    "CH3NO": ATOM_MASSES["C"] + (ATOM_MASSES["H"] * 3) + ATOM_MASSES["N"] + ATOM_MASSES["O"],
+    "CH4O": ATOM_MASSES["C"] + (ATOM_MASSES["H"] * 4) + ATOM_MASSES["O"],
+    "CH4SO": ATOM_MASSES["C"] + (ATOM_MASSES["H"] * 4) + ATOM_MASSES["S"] + ATOM_MASSES["O"],
+    "CO2": ATOM_MASSES["C"] + (ATOM_MASSES["O"] * 2),
+    "H2O": (ATOM_MASSES["H"] * 2) + ATOM_MASSES["O"],
+    "NH3": ATOM_MASSES["N"] + (ATOM_MASSES["H"] * 3),
+    "H3O4P": (ATOM_MASSES["H"] * 3) + (ATOM_MASSES["O"] * 4) + ATOM_MASSES["P"],
+}
+
+Unimod_Neutral_losses = {7: ["CHNO"], 21: ["H3O4P"]}
+
 #######################################
 # HELPERS FOR FRAGMENT MZ CALCULATION #
 #######################################
@@ -339,6 +399,7 @@
     "PRECURSOR_MASS_EXP",
     "SCORE",
     "REVERSE",
+    "PROTEINS",
 ]
 META_DATA_COLUMNS = SHARED_DATA_COLUMNS + META_DATA_ONLY_COLUMNS
 MZML_ONLY_DATA_COLUMNS = [
@@ -384,36 +445,89 @@
     "[UNIMOD:35]": "[Oxidation (O)]",
 }
 
-FRAGMENTATION_ENCODING = {"HCD": 2, "CID": 1}
+FRAGMENTATION_ENCODING = {
+    "CID": 1,
+    "HCD": 2,
+    "ETD": 3,
+    "ETHCD": 4,
+    "ETCID": 5,
+    "UVPD": 6,
+    "EID": 7,
+    "ECD": 8,
+    "AIECD": 9,
+}
+
+########################
+# RESCORING PARAMETERS #
+########################
+
+
+class RescoreType(Enum):
+    """Class for rescoring types."""
+
+    PROSIT = "prosit"
+    ANDROMEDA = "andromeda"
+
+
+#############
+# ION TYPES #
+#############
+FORWARD_IONS = ["a", "b", "c"]
+BACKWARDS_IONS = ["x", "y", "z", "z_r"]  #
+IONS = FORWARD_IONS + BACKWARDS_IONS
+
+FRAGMENTATION_TO_IONS_BY_PAIRS = {
+    "HCD": [BACKWARDS_IONS[1], FORWARD_IONS[1]],  # y,b
+    "CID": [BACKWARDS_IONS[1], FORWARD_IONS[1]],  # y,b
+    "ETD": [BACKWARDS_IONS[-1], FORWARD_IONS[2]],  # z_r,c
+    "ECD": [BACKWARDS_IONS[-1], FORWARD_IONS[2]],  # z_r,c
+    "ETHCD": [BACKWARDS_IONS[1], FORWARD_IONS[1], BACKWARDS_IONS[-1], FORWARD_IONS[2]],  # y,b,z_r,c
+    "ETCID": [BACKWARDS_IONS[1], FORWARD_IONS[1], BACKWARDS_IONS[-1], FORWARD_IONS[2]],  # y,b,z_r,c
+    "UVPD": [
+        BACKWARDS_IONS[0],
+        FORWARD_IONS[0],
+        BACKWARDS_IONS[1],
+        FORWARD_IONS[1],
+        BACKWARDS_IONS[2],
+        FORWARD_IONS[2],
+    ],  # y,b,z,c,x,a
+}
+
+FRAGMENTATION_TO_IONS_BY_DIRECTION = {
+    "HCD": [BACKWARDS_IONS[1], FORWARD_IONS[1]],  # y,b
+    "CID": [BACKWARDS_IONS[1], FORWARD_IONS[1]],  # y,b
+    "ETD": [BACKWARDS_IONS[-1], FORWARD_IONS[2]],  # z_r,c
+    "ECD": [BACKWARDS_IONS[-1], FORWARD_IONS[2]],  # z_r,c
+    "ETHCD": [BACKWARDS_IONS[1], BACKWARDS_IONS[-1]] + FORWARD_IONS[1:],  # y,z_r,b,c
+    "ETCID": [BACKWARDS_IONS[1], BACKWARDS_IONS[-1]] + FORWARD_IONS[1:],  # y,z_r,b,c
+    "UVPD": BACKWARDS_IONS[:-1] + FORWARD_IONS,  # y,z,x,b,c,a
+}
+
+ION_DELTAS = {
+    "a": -ATOM_MASSES["O"] - ATOM_MASSES["C"],
+    "b": 0.0,
+    "c": 3 * ATOM_MASSES["H"] + ATOM_MASSES["N"],
+    "x": 2 * ATOM_MASSES["O"] + ATOM_MASSES["C"],
+    "y": ATOM_MASSES["O"] + 2 * ATOM_MASSES["H"],
+    "z": ATOM_MASSES["O"] - ATOM_MASSES["N"] - ATOM_MASSES["H"],
+    "z_r": ATOM_MASSES["O"] - ATOM_MASSES["N"],
+}
 
 ############################
 # GENERATION OF ANNOTATION #
 ############################
 
-IONS = ["y", "b"]  # limited to single character unicode string when array is created
 CHARGES = [1, 2, 3]  # limited to uint8 (0-255) when array is created
 POSITIONS = [x for x in range(1, 30)]  # fragment numbers 1-29 -- limited to uint8 (0-255) when array is created
-
+POSITIONS_XL = [x for x in range(1, 59)]
 ANNOTATION_FRAGMENT_TYPE = []
 ANNOTATION_FRAGMENT_CHARGE = []
 ANNOTATION_FRAGMENT_NUMBER = []
 for pos in POSITIONS:
-    for ion in IONS:
+    for ion in FRAGMENTATION_TO_IONS_BY_DIRECTION["HCD"]:
         for charge in CHARGES:
             ANNOTATION_FRAGMENT_TYPE.append(ion)
             ANNOTATION_FRAGMENT_CHARGE.append(charge)
             ANNOTATION_FRAGMENT_NUMBER.append(pos)
 
 ANNOTATION = [ANNOTATION_FRAGMENT_TYPE, ANNOTATION_FRAGMENT_CHARGE, ANNOTATION_FRAGMENT_NUMBER]
-
-
-########################
-# RESCORING PARAMETERS #
-########################
-
-
-class RescoreType(Enum):
-    """Class for rescoring types."""
-
-    PROSIT = "prosit"
-    ANDROMEDA = "andromeda"
diff --git a/spectrum_fundamentals/fragments.py b/spectrum_fundamentals/fragments.py
index b781e75..a029d5c 100644
--- a/spectrum_fundamentals/fragments.py
+++ b/spectrum_fundamentals/fragments.py
@@ -1,18 +1,20 @@
+import itertools
 import logging
 import re
 from operator import itemgetter
-from typing import Dict, List, Optional, Tuple
+from typing import Dict, List, Literal, Optional, Tuple, Union
 
 import numpy as np
 import pandas as pd
 
-from . import constants as constants
+import spectrum_fundamentals.constants as c
+
 from .mod_string import internal_without_mods
 
 logger = logging.getLogger(__name__)
 
 
-def _get_modifications(peptide_sequence: str) -> Dict[int, float]:
+def _get_modifications(peptide_sequence: str, custom_mods: Optional[Dict[str, float]] = None) -> Dict[int, float]:
     """
     Get modification masses and position in a peptide sequence.
 
@@ -24,6 +26,7 @@ def _get_modifications(peptide_sequence: str) -> Dict[int, float]:
     modification was present are returned.
 
     :param peptide_sequence: Modified peptide sequence
+    :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
     :return: modification_deltas
     """
     modification_deltas = {}
@@ -37,37 +40,39 @@ def _get_modifications(peptide_sequence: str) -> Dict[int, float]:
     pattern = re.compile(r"\[.{8}[^\]]*\]")
     matches = pattern.finditer(peptide_sequence)
 
+    mod_masses = c.MOD_MASSES | (custom_mods or {})
+
     for match in matches:
-        start_pos = match.start()
-        end_pos = match.end()
-        modification_deltas[start_pos - offset] = constants.MOD_MASSES[peptide_sequence[start_pos:end_pos]]
+        start_pos, end_pos = match.span()
+        modification_deltas[start_pos - offset] = mod_masses[match.group()]
         offset += end_pos - start_pos
 
     return modification_deltas
 
 
-def compute_peptide_mass(sequence: str) -> float:
+def compute_peptide_mass(sequence: str, custom_mods: Optional[Dict[str, float]] = None) -> float:
     """
     Compute the theoretical mass of the peptide sequence.
 
     :param sequence: Modified peptide sequence
+    :param custom_mods: Custom Modifications with the identifier, the unimod equivalent and the respective mass
     :return: Theoretical mass of the sequence
     """
-    terminal_masses = 2 * constants.ATOM_MASSES["H"] + constants.ATOM_MASSES["O"]  # add terminal masses HO- and H-
+    terminal_masses = 2 * c.ATOM_MASSES["H"] + c.ATOM_MASSES["O"]  # add terminal masses HO- and H-
 
-    modification_deltas = _get_modifications(sequence)
+    modification_deltas = _get_modifications(sequence, custom_mods=custom_mods)
     if modification_deltas:  # there were modifictions
         sequence = internal_without_mods([sequence])[0]
         terminal_masses += modification_deltas.get(-2, 0.0)  # prime with n_term_mod delta if present
 
-    peptide_sum = sum([constants.AA_MASSES[c] + modification_deltas.get(i, 0.0) for i, c in enumerate(sequence)])
+    peptide_sum = sum([c.AA_MASSES[aa] + modification_deltas.get(i, 0.0) for i, aa in enumerate(sequence)])
 
     return terminal_masses + peptide_sum
 
 
 def _xl_sanity_check(noncl_xl: int, peptide_beta_mass: float, xl_pos: float):
     """
-    Checks input validity for initialize_peacks when used with xl mode.
+    Checks input validity for initialize_peaks when used with xl mode.
 
     :param noncl_xl: whether the function is called with a non-cleavable xl modification
     :param peptide_beta_mass: the mass of the second peptide to be considered for non-cleavable XL
@@ -81,7 +86,134 @@ def _xl_sanity_check(noncl_xl: int, peptide_beta_mass: float, xl_pos: float):
             raise ValueError("Crosslinker position must be provided if using non cleavable XL mode.")
 
 
-def initialize_peaks(
+def retrieve_ion_types(fragmentation_method: str) -> List[str]:
+    """
+    Retrieve the ion types resulting from a fragmentation method in the correct order for dlomix predictions.
+
+    Given the fragmentation method the function returns all ion types that can result from it.
+
+    :param fragmentation_method: fragmentation method used during the MS
+    :raises ValueError: if fragmentation_method is not supported
+    :return: list of possible ion types
+    """
+    fragmentation_method = fragmentation_method.upper()
+    ions = c.FRAGMENTATION_TO_IONS_BY_PAIRS.get(fragmentation_method, [])
+    if not ions:
+        raise ValueError(f"Unknown fragmentation method provided: {fragmentation_method}")
+    return ions
+
+
+def retrieve_ion_types_for_peak_initialization(fragmentation_method: str) -> List[str]:
+    """
+    Retrieve the ion types resulting from a fragmentation method in the correct order for peak initialization.
+
+    Given the fragmentation method the function returns all ion types that can result from it.
+
+    :param fragmentation_method: fragmentation method used during the MS
+    :raises ValueError: if fragmentation_method is not supported
+    :return: list of possible ion types
+    """
+    fragmentation_method = fragmentation_method.upper()
+    ions = c.FRAGMENTATION_TO_IONS_BY_DIRECTION.get(fragmentation_method, [])
+    if not ions:
+        raise ValueError(f"Unknown fragmentation method provided: {fragmentation_method}")
+    return ions
+
+
+def get_ion_delta(ion_types: List[str]) -> np.ndarray:
+    """
+    Calculate the mass of an ion.
+
+    :param ion_types: type of ions for which mass should be calculated
+    :return: numpy array with masses of the ions
+    """
+    return np.array([c.ION_DELTAS[ion_type] for ion_type in ion_types]).reshape(len(ion_types), 1)
+
+
+def _add_nl(neutral_losses: List[str], nl_dict: dict, start_aa_index: int, end_aa_index: int):
+    """
+    Adds neutral losses (NL) to a dictionary of neutral losses for specific amino acid indices.
+
+    This function updates the `nl_dict` by incorporating the provided `neutral_losses` into
+    the amino acid indices between `start_aa_index` and `end_aa_index`.
+
+    :param neutral_losses: A list of neutral losses to be added to the amino acids.
+    :param nl_dict: A dictionary where the keys are amino acid indices and the values are lists of neutral
+        losses associated with each index.
+    :param start_aa_index: The starting index of the amino acid range to which the neutral losses should be added.
+    :param end_aa_index: The ending index of the amino acid range to which the neutral losses should be added.
+    :returns: Updated dictionary with the added neutral losses for the specified amino acid indices.
+    """
+    first_nl = True
+    new_nls = {}
+    for nl in neutral_losses:
+        for i in range(start_aa_index, end_aa_index):
+            current_aa_nl = nl_dict[i]
+            if first_nl:
+                new_nls[i] = list(set(neutral_losses) - set(current_aa_nl))
+            if nl not in current_aa_nl:
+                current_aa_nl.append(nl)
+        first_nl = False
+    return nl_dict
+
+
+def _get_neutral_losses(peptide_sequence, modifications):
+    """
+    Get possible neutral losses and position in a peptide sequence.
+
+    :param peptide_sequence: Unmodified peptide sequence
+    :param modifications: modifications dict generated by _get_modifications from modified petide sequence.
+    :return: Dict with neutral losses position as an ID and composition as its value.
+    """
+    sequence_length = len(peptide_sequence)
+    keys = range(0, sequence_length - 1)
+
+    nl_b_ions = {key: [] for key in keys}
+    nl_y_ions = {key: [] for key in keys}
+
+    for i in range(0, sequence_length):
+        aa = peptide_sequence[i]
+        if aa in c.AA_Neutral_losses:
+            if i in modifications:
+                """if aa == "M" and modifications[i] == 15.9949146:
+                nl_b_ions = _add_nl(c.AA_Neutral_losses["M[UNIMOD:35]"], nl_b_ions, i, sequence_length - 1)
+                nl_y_ions = _add_nl(
+                    c.AA_Neutral_losses["M[UNIMOD:35]"], nl_y_ions, sequence_length - i - 1, sequence_length - 1
+                )"""
+                if aa == "R" and modifications[i] == 0.984016:
+                    nl_b_ions = _add_nl(c.Mod_Neutral_losses["R[UNIMOD:7]"], nl_b_ions, i, sequence_length - 1)
+                    nl_y_ions = _add_nl(
+                        c.Mod_Neutral_losses["R[UNIMOD:7]"], nl_y_ions, sequence_length - i - 1, sequence_length - 1
+                    )
+                elif (aa == "S" or aa == "T") and modifications[i] == 79.966331:
+                    nl_b_ions = _add_nl(c.Mod_Neutral_losses["S[UNIMOD:21]"], nl_b_ions, i, sequence_length - 1)
+                    nl_y_ions = _add_nl(
+                        c.Mod_Neutral_losses["S[UNIMOD:21]"], nl_y_ions, sequence_length - i - 1, sequence_length - 1
+                    )
+            """else:
+                nl_b_ions = _add_nl(c.AA_Neutral_losses[aa], nl_b_ions, i, sequence_length - 1)
+                nl_y_ions = _add_nl(c.AA_Neutral_losses[aa], nl_y_ions, sequence_length - i - 1, sequence_length - 1)"""
+    return nl_b_ions, nl_y_ions
+
+
+def _calculate_nl_score_mass(neutral_loss):
+    """
+    Calculates the score and mass for a given neutral loss (NL).
+
+    :param neutral_loss: The type of neutral loss for which to calculate the score and mass.
+    :returns: A tuple containing the adjusted score and the mass of the specified neutral loss.
+    """
+    score = 100
+    mass = 0
+    mass = c.Neutral_losses_Mass[neutral_loss]
+    if neutral_loss == "H2O" or neutral_loss == "NH3":
+        score -= 5
+    else:
+        score -= 30
+    return score, mass
+
+
+def initialize_peaks(  # noqa: C901
     sequence: str,
     mass_analyzer: str,
     charge: int,
@@ -90,7 +222,10 @@ def initialize_peaks(
     noncl_xl: bool = False,
     peptide_beta_mass: float = 0.0,
     xl_pos: int = -1,
-) -> Tuple[List[dict], int, str, float]:
+    fragmentation_method: str = "HCD",
+    custom_mods: Optional[Dict[str, float]] = None,
+    add_neutral_losses: Optional[bool] = False,
+) -> Tuple[List[dict], int, str, float, int]:
     """
     Generate theoretical peaks for a modified peptide sequence.
 
@@ -102,88 +237,109 @@ def initialize_peaks(
     :param noncl_xl: whether the function is called with a non-cleavable xl modification
     :param peptide_beta_mass: the mass of the second peptide to be considered for non-cleavable XL
     :param xl_pos: the position of the crosslinker for non-cleavable XL
-    :return: List of theoretical peaks, Flag to indicate if there is a tmt on n-terminus, Un modified peptide sequence
+    :param fragmentation_method: fragmentation method that was used
+    :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
+    :param add_neutral_losses: Flag to indicate whether to annotate neutral losses or not
+    :return: List of theoretical peaks, Flag to indicate if there is a tmt on n-terminus, Un modified peptide sequence,
+        number of expected nl peaks
     """
     _xl_sanity_check(noncl_xl, peptide_beta_mass, xl_pos)
 
     max_charge = min(3, charge)
-    ion_type_offsets = [0.0, constants.ATOM_MASSES["O"] + 2 * constants.ATOM_MASSES["H"]]
-
-    # tmp place holder
-    ion_type_masses = [0.0, 0.0]
-    ion_types = ["b", "y"]
+    ion_types = retrieve_ion_types_for_peak_initialization(fragmentation_method)
+    modification_deltas = _get_modifications(sequence, custom_mods=custom_mods)
 
-    number_of_ion_types = len(ion_type_offsets)
     fragments_meta_data = []
-
-    modification_deltas = _get_modifications(sequence)
-    forward_sum = 0.0  # sum over all amino acids from left to right (neutral charge)
-    backward_sum = 0.0  # sum over all amino acids from right to left (neutral charge)
     n_term_mod = 1
+
+    if noncl_xl:
+        # the test only needs to be done because the unit tests use non_cl_xl peptides
+        # without a crosslinker modification. This cannot occur in nature!!!
+        # The unit tests need to be changed, then we can simply add to the existing
+        # modification mass at xl_pos -1.
+        modification_deltas[xl_pos - 1] = modification_deltas.get(xl_pos - 1, 0.0) + peptide_beta_mass
+
     if modification_deltas:  # there were modifictions
         sequence = internal_without_mods([sequence])[0]
-        n_term_delta = modification_deltas.get(-2, 0.0)
+        n_term_delta = modification_deltas.pop(-2, 0.0)  # directly pop it to avoid readding it later
         if n_term_delta != 0:
             n_term_mod = 2
             # add n_term mass to first aa for easy processing in the following calculation
             modification_deltas[0] = modification_deltas.get(0, 0.0) + n_term_delta
 
-    # calculation:
-
-    peptide_length = len(sequence)
-    for i in range(peptide_length):  # generate substrings
-        forward_sum += constants.AA_MASSES[sequence[i]]  # sum left to right
-        if i in modification_deltas:  # add mass of modification if present
-            forward_sum += modification_deltas[i]
-        backward_sum += constants.AA_MASSES[sequence[peptide_length - i - 1]]  # sum right to left
-        if peptide_length - i - 1 in modification_deltas:  # add mass of modification if present
-            backward_sum += modification_deltas[peptide_length - i - 1]
-
-        ion_type_masses[0] = forward_sum + ion_type_offsets[0]  # b ion - ...
-
-        ion_type_masses[1] = backward_sum + ion_type_offsets[1]  # y ion
-
-        for charge in range(constants.MIN_CHARGE, max_charge + 1):  # generate ion in different charge states
-            # positive charge is introduced by protons (or H - ELECTRON_MASS)
-            charge_delta = charge * constants.PARTICLE_MASSES["PROTON"]
-            for ion_type in range(number_of_ion_types):  # generate all ion types
-                mass = _compute_ion_mass(
-                    ion_mass=ion_type_masses[ion_type],
-                    noncl_xl=noncl_xl,
-                    ion_type=ion_type,
-                    xl_pos=xl_pos,
-                    peptide_beta_mass=peptide_beta_mass,
-                    peptide_length=peptide_length,
-                    i=i,
-                )
-                mz = (mass + charge_delta) / charge
-                min_mz, max_mz = get_min_max_mass(mass_analyzer, mz, mass_tolerance, unit_mass_tolerance)
-
+    if add_neutral_losses:
+        nl_b_ions, nl_y_ions = _get_neutral_losses(sequence, modification_deltas)
+        nl_ions = [nl_y_ions, nl_b_ions]
+
+    expected_nl_count = 0
+    mass_arr = np.array([c.AA_MASSES[_] for _ in sequence])
+    for pos, mod_mass in modification_deltas.items():
+        mass_arr[pos] += mod_mass
+
+    n_forward_ions = len(ion_types) // 2
+    n_fragments = len(sequence) - 1
+    sum_array = np.empty(shape=(len(ion_types), n_fragments))
+    np.cumsum(mass_arr[:0:-1], out=sum_array[0])  # this is for the reverse ion-series
+    np.cumsum(mass_arr[:-1], out=sum_array[n_forward_ions])  # this is for the forward ion-series
+    peptide_mass = sum_array[0, -1] + mass_arr[0]  # this is the longest reverse ion + the first residue
+
+    # get offset for all needed ions
+    deltas = get_ion_delta(ion_types)
+    np.add(sum_array[0], deltas[:n_forward_ions], out=sum_array[:n_forward_ions])
+    np.add(sum_array[n_forward_ions], deltas[n_forward_ions:], out=sum_array[n_forward_ions:])
+
+    # calculate for m/z for charges 1, 2, 3
+    # shape of ion_mzs: (n_ions, n_fragments, max_charge)
+    charges = np.arange(1, max_charge + 1)
+    ion_mzs = (sum_array[..., np.newaxis] + charges * c.PARTICLE_MASSES["PROTON"]) / charges
+    min_mzs, max_mzs = get_min_max_mass(mass_analyzer, ion_mzs, mass_tolerance, unit_mass_tolerance)
+
+    # write mz together with min and max value in output list with one dictionary for each ion
+    for ion_type in range(len(ion_types)):
+        for number in range(n_fragments):
+            for charge in range(max_charge):
                 fragments_meta_data.append(
                     {
                         "ion_type": ion_types[ion_type],  # ion type
-                        "no": i + 1,  # no
-                        "charge": charge,  # charge
-                        "mass": mz,  # mz
-                        "min_mass": min_mz,  # min mz
-                        "max_mass": max_mz,  # max mz
+                        "no": number + 1,  # no
+                        "charge": charge + 1,  # charge
+                        "mass": ion_mzs[ion_type, number, charge],  # mz
+                        "min_mass": min_mzs[ion_type, number, charge],  # min mz
+                        "max_mass": max_mzs[ion_type, number, charge],  # max mz
+                        "neutral_loss": "",
+                        "fragment_score": 100,
                     }
                 )
-    fragments_meta_data = sorted(fragments_meta_data, key=itemgetter("mass"))
-    return fragments_meta_data, n_term_mod, sequence, (forward_sum + ion_type_offsets[0] + ion_type_offsets[1])
-
-
-def _compute_ion_mass(
-    ion_mass: float, noncl_xl: bool, ion_type: int, xl_pos: int, peptide_beta_mass: float, peptide_length: int, i: int
-) -> float:
-    # Check for neutral loss here
+                if not add_neutral_losses:
+                    continue
+                for nl in nl_ions[ion_type][number]:
+                    nl_score, nl_mass = _calculate_nl_score_mass(nl)
+                    ion_mass = sum_array[ion_type, number] - nl_mass
+                    ion_mz = (ion_mass + (charge + 1) * c.PARTICLE_MASSES["PROTON"]) / (charge + 1)
+                    min_mz, max_mz = get_min_max_mass(mass_analyzer, ion_mz, mass_tolerance, unit_mass_tolerance)
+                    expected_nl_count += 1
+                    fragments_meta_data.append(
+                        {
+                            "ion_type": ion_types[ion_type],  # ion type
+                            "no": number + 1,  # no
+                            "charge": charge + 1,  # charge
+                            "mass": ion_mz,  # mz
+                            "min_mass": min_mz,  # min mz
+                            "max_mass": max_mz,  # max mz
+                            "neutral_loss": nl,
+                            "fragment_score": 100 - nl_score,
+                        }
+                    )
 
-    if noncl_xl and ((ion_type == 0 and i + 1 >= xl_pos) or (ion_type == 1 and i >= peptide_length - xl_pos)):
-        mass = ion_mass + peptide_beta_mass
-    else:
-        mass = ion_mass
+    fragments_meta_data = sorted(fragments_meta_data, key=itemgetter("mass"))
 
-    return mass
+    return (
+        fragments_meta_data,
+        n_term_mod,
+        sequence,
+        (peptide_mass + c.ATOM_MASSES["O"] + 2 * c.ATOM_MASSES["H"]),
+        expected_nl_count,
+    )
 
 
 def initialize_peaks_xl(
@@ -194,6 +350,7 @@ def initialize_peaks_xl(
     mass_tolerance: Optional[float] = None,
     unit_mass_tolerance: Optional[str] = None,
     sequence_beta: Optional[str] = None,
+    custom_mods: Optional[Dict[str, float]] = None,
 ) -> Tuple[List[dict], int, str, float]:
     """
     Generate theoretical peaks for a modified (potentially cleavable cross-linked) peptide sequence.
@@ -207,6 +364,7 @@ def initialize_peaks_xl(
     :param mass_tolerance: mass tolerance to calculate min and max mass
     :param unit_mass_tolerance: unit for the mass tolerance (da or ppm)
     :param sequence_beta: optional second peptide to be considered for non-cleavable XL
+    :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
     :raises ValueError: if crosslinker_type is unkown
     :raises AssertionError: if the short and long XL sequence (the one with the short / long crosslinker mod)
         has a tmt n term while the other one does not
@@ -241,11 +399,11 @@ def initialize_peaks_xl(
         # the crosslinker is returned! This needs to be fixed, because mass is used as CALCULATED_MASS in
         # percolator!
 
-        list_out_s, tmt_n_term_s, peptide_sequence, _ = initialize_peaks(
-            sequence_s, mass_analyzer, charge, mass_tolerance, unit_mass_tolerance
+        list_out_s, tmt_n_term_s, peptide_sequence, _, _ = initialize_peaks(
+            sequence_s, mass_analyzer, charge, mass_tolerance, unit_mass_tolerance, custom_mods=custom_mods
         )
-        list_out_l, tmt_n_term_l, peptide_sequence, _ = initialize_peaks(
-            sequence_l, mass_analyzer, charge, mass_tolerance, unit_mass_tolerance
+        list_out_l, tmt_n_term_l, peptide_sequence, _, _ = initialize_peaks(
+            sequence_l, mass_analyzer, charge, mass_tolerance, unit_mass_tolerance, custom_mods=custom_mods
         )
 
         tmt_n_term = tmt_n_term_s
@@ -279,7 +437,7 @@ def initialize_peaks_xl(
         sequence_mass = compute_peptide_mass(sequence_without_crosslinker)
         sequence_beta_mass = compute_peptide_mass(sequence_beta_without_crosslinker)
 
-        list_out, tmt_n_term, peptide_sequence, _ = initialize_peaks(
+        list_out, tmt_n_term, peptide_sequence, _, _ = initialize_peaks(
             sequence,
             mass_analyzer,
             charge,
@@ -288,6 +446,7 @@ def initialize_peaks_xl(
             True,
             sequence_beta_mass if sequence_beta_mass is not None else None,
             crosslinker_position,
+            custom_mods=custom_mods,
         )
         df_out = pd.DataFrame(list_out)
 
@@ -309,8 +468,11 @@ def initialize_peaks_xl(
 
 
 def get_min_max_mass(
-    mass_analyzer: str, mass: float, mass_tolerance: Optional[float] = None, unit_mass_tolerance: Optional[str] = None
-) -> Tuple[float, float]:
+    mass_analyzer: str,
+    mass: np.ndarray,
+    mass_tolerance: Optional[float] = None,
+    unit_mass_tolerance: Optional[str] = None,
+) -> Tuple[np.ndarray, np.ndarray]:
     """Helper function to get min and max mass based on mass analyzer.
 
     If both mass_tolerance and unit_mass_tolerance are provided, the function uses the provided tolerance
@@ -354,108 +516,51 @@ def get_min_max_mass(
     return (min_mass, max_mass)
 
 
-def compute_ion_masses(seq_int: List[int], charge_onehot: List[int], tmt: str = "") -> Optional[np.ndarray]:
-    """
-    Collects an integer sequence e.g. [1,2,3] with charge 2 and returns array with 174 positions for ion masses.
+FragmentIonComponent = Literal["ion_type", "position", "charge"]
+
 
-    Invalid masses are set to -1.
+def generate_fragment_ion_annotations(
+    ion_types: List[str], order: Tuple[FragmentIonComponent, FragmentIonComponent, FragmentIonComponent]
+) -> List[Tuple[str, int, int]]:
+    """Generate full list of fragment ions for permitted ion types and specified order.
 
-    :param seq_int: TODO
-    :param charge_onehot: is a onehot representation of charge with 6 elems for charges 1 to 6
-    :param tmt: TODO
-    :return: list of masses as floats
+    :param ion_types: List of permitted ion types
+    :param order: What fragment ion parameters (ion type, position & charge) to group the annotations by
+    :return: List of (ion_type, position, charge) tuples sorted by specified component order
+    :raises ValueError: if invalid or unsupported ion types are specified or duplicate order keys are used
     """
-    charge = list(charge_onehot).index(1) + 1
-    if not (charge in (1, 2, 3, 4, 5, 6) and len(charge_onehot) == 6):
-        print("[ERROR] One-hot-enconded Charge is not in valid range 1 to 6")
-        return None
-
-    if not len(seq_int) == constants.SEQ_LEN:
-        print(f"[ERROR] Sequence length {len(seq_int)} is not desired length of {constants.SEQ_LEN}")
-        return None
-
-    idx = list(seq_int).index(0) if 0 in seq_int else constants.SEQ_LEN
-    masses = np.ones((constants.SEQ_LEN - 1) * 2 * 3, dtype=np.float32) * -1
-    mass_b = 0
-    mass_y = 0
-    j = 0  # iterate over masses
-
-    # Iterate over sequence, sequence should have length 30
-    for i in range(idx - 1):  # only 29 possible ions
-        j = i * 6  # index for masses array at position
-
-        # MASS FOR Y IONS
-        # print("Added", constants.VEC_MZ[seq_int[l-1-i]])
-        mass_y += constants.VEC_MZ[seq_int[idx - 1 - i]]
-
-        # Compute charge +1
-        masses[j] = (
-            mass_y
-            + 1 * constants.PARTICLE_MASSES["PROTON"]
-            + constants.MASSES["C_TERMINUS"]
-            + constants.ATOM_MASSES["H"]
-        ) / 1.0
-        # Compute charge +2
-        masses[j + 1] = (
-            (
-                mass_y
-                + 2 * constants.PARTICLE_MASSES["PROTON"]
-                + constants.MASSES["C_TERMINUS"]
-                + constants.ATOM_MASSES["H"]
-            )
-            / 2.0
-            if charge >= 2
-            else -1.0
-        )
-        # Compute charge +3
-        masses[j + 2] = (
-            (
-                mass_y
-                + 3 * constants.PARTICLE_MASSES["PROTON"]
-                + constants.MASSES["C_TERMINUS"]
-                + constants.ATOM_MASSES["H"]
-            )
-            / 3.0
-            if charge >= 3.0
-            else -1.0
+    fragment_ion_components: Dict[str, Union[List[str]]] = {
+        "ion_type": ion_types,
+        "position": [str(pos) for pos in c.POSITIONS],
+        "charge": [str(charge) for charge in c.CHARGES],
+    }
+
+    if len(set(ion_types)) != len(ion_types):
+        raise ValueError("Redundant ion types specified")
+    elif len(ion_types) == 0:
+        raise ValueError("No ion types specified")
+    if set(order) != {"ion_type", "position", "charge"}:
+        raise ValueError("Duplicate component used for ordering fragment ions")
+
+    raw_annotations = list(itertools.product(*[fragment_ion_components[component] for component in order]))
+
+    ordered_raw_annotations = [
+        (
+            str(combination[order.index("ion_type")]),
+            int(combination[order.index("position")]),
+            int(combination[order.index("charge")]),
         )
+        for combination in raw_annotations
+    ]
 
-        # MASS FOR B IONS
-        if i == 0 and tmt != "":
-            mass_b += constants.VEC_MZ[seq_int[i]] + constants.MOD_MASSES[constants.TMT_MODS[tmt]]
-        else:
-            mass_b += constants.VEC_MZ[seq_int[i]]
-
-        # Compute charge +1
-        masses[j + 3] = (
-            mass_b
-            + 1 * constants.PARTICLE_MASSES["PROTON"]
-            + constants.MASSES["N_TERMINUS"]
-            - constants.ATOM_MASSES["H"]
-        ) / 1.0
-        # Compute charge +2
-        masses[j + 4] = (
-            (
-                mass_b
-                + 2 * constants.PARTICLE_MASSES["PROTON"]
-                + constants.MASSES["N_TERMINUS"]
-                - constants.ATOM_MASSES["H"]
-            )
-            / 2.0
-            if charge >= 2
-            else -1.0
-        )
-        # Compute charge +3
-        masses[j + 5] = (
-            (
-                mass_b
-                + 3 * constants.PARTICLE_MASSES["PROTON"]
-                + constants.MASSES["N_TERMINUS"]
-                - constants.ATOM_MASSES["H"]
-            )
-            / 3.0
-            if charge >= 3.0
-            else -1.0
-        )
+    return ordered_raw_annotations
 
-    return masses
+
+def format_fragment_ion_annotation(raw_annotation: Tuple[str, int, int]) -> str:
+    """Transform (ion_type, position, charge) tuple into <ion_type><position>+<charge> string.
+
+    :param raw_annotation: `(ion_type, position, charge)` tuple
+    :returns: formatted annotation string
+    """
+    ion_type, pos, charge = raw_annotation
+    return f"{ion_type}{pos}+{charge}"
diff --git a/spectrum_fundamentals/metrics/percolator.py b/spectrum_fundamentals/metrics/percolator.py
index 1d4455d..e10909d 100644
--- a/spectrum_fundamentals/metrics/percolator.py
+++ b/spectrum_fundamentals/metrics/percolator.py
@@ -57,16 +57,47 @@ def __init__(
         all_features_flag: bool = False,
         regression_method: str = "lowess",
         fdr_cutoff: float = 0.01,
+        additional_columns: Optional[Union[str, list]] = None,
+        neutral_loss_flag: Optional[bool] = False,
+        drop_miss_cleavage_flag: Optional[bool] = False,
     ):
         """Initialize a Percolator obj."""
+        super().__init__(pred_intensities, true_intensities, mz, "CROSSLINKER_TYPE" in metadata.columns)
+
         self.metadata = metadata
         self.input_type = input_type
         self.all_features_flag = all_features_flag
+        self.additional_columns = additional_columns
         self.regression_method = regression_method
         self.fdr_cutoff = fdr_cutoff
-        self.xl = "CROSSLINKER_TYPE" in self.metadata.columns
-
-        super().__init__(pred_intensities, true_intensities, mz)
+        self.neutral_loss_flag = neutral_loss_flag
+        self.drop_miss_cleavage_flag = drop_miss_cleavage_flag
+
+        self.base_columns = [
+            "raw_file",
+            "scan_number",
+            "modified_sequence",
+            "precursor_charge",
+            "scan_event_number",
+            "mass",
+            "score",
+            "reverse",
+            "sequence",
+            "peptide_length",
+            "fragmentation",
+            "calculated_mass",
+            "sequence_a",
+            "sequence_b",
+            "modified_sequence_a",
+            "modified_sequence_b",
+            "retention_time",
+            "predicted_irt",
+            "instrument_types",
+            "mass_analyzer",
+            "mz_range",
+            "collision_energy",
+            "proteins",
+        ]
 
     @staticmethod
     def sample_balanced_over_bins(retention_time_df: pd.DataFrame, sample_size: int = 5000) -> pd.Index:
@@ -140,7 +171,7 @@ def get_aligned_predicted_retention_times(
                 observed_rts = observed_rts[keep_idxs[0]]
                 predicted_rts = predicted_rts[keep_idxs[0]]
 
-                discard_percentage *= 1.5
+                discard_percentage *= 1.2
 
         logger.debug(f"Observed RT anchor points:\n{observed_retention_times_fdr_filtered}")
         logger.debug(f"Predicted RT anchor points:\n{predicted_retention_times_fdr_filtered}")
@@ -274,23 +305,39 @@ def add_common_features(self):
         self.metrics_val["HCD"] = (self.metadata["FRAGMENTATION"] == "HCD").astype(int)
         self.metrics_val["CID"] = (self.metadata["FRAGMENTATION"] == "CID").astype(int)
 
+    def add_additional_features(self):
+        """Add additional features from custom serch results if specified."""
+        feature_cols = []
+
+        if isinstance(self.additional_columns, list):
+            feature_cols = self.additional_columns
+        elif isinstance(self.additional_columns, str) and (self.additional_columns.lower() == "all"):
+            feature_cols = [x for x in self.metadata.columns if x.lower() not in set(self.base_columns)]
+            feature_cols = [x for x in feature_cols if not x.lower().startswith("unnamed")]  # remove Unnamed cols
+
+        for col in feature_cols:
+            if col not in self.metadata.columns:
+                raise ValueError(f"provided column: {col} cannot be found in search results.")
+            elif not pd.api.types.is_numeric_dtype(self.metadata[col]):
+                raise ValueError(f"wrong datatype for column: {col}, datatype must be numerical.")
+            else:
+                self.metrics_val[col] = self.metadata[col]
+
     def add_percolator_metadata_columns(self):
         """Add metadata columns needed by percolator, e.g. to identify a PSM."""
         if self.xl:
             spec_id_cols = ["RAW_FILE", "SCAN_NUMBER", "MODIFIED_SEQUENCE_A", "MODIFIED_SEQUENCE_B", "PRECURSOR_CHARGE"]
-            self.metrics_val["Peptide"] = (
-                self.metadata["MODIFIED_SEQUENCE_A"] + "_" + self.metadata["MODIFIED_SEQUENCE_B"]
-            ).apply(lambda x: "_." + x + "._")
-            self.metrics_val["Proteins"] = (
-                self.metadata["MODIFIED_SEQUENCE_A"] + "_" + self.metadata["MODIFIED_SEQUENCE_B"]
+            modified_sequence_a = self.metadata["MODIFIED_SEQUENCE_A"].astype(str)
+            modified_sequence_b = self.metadata["MODIFIED_SEQUENCE_B"].astype(str)
+            self.metrics_val["Peptide"] = (modified_sequence_a + "_" + modified_sequence_b).apply(
+                lambda x: "_." + x + "._"
             )
+            self.metrics_val["Proteins"] = modified_sequence_a + "_" + modified_sequence_b
             self.metrics_val["Label"] = self.target_decoy_labels
         else:
             spec_id_cols = ["RAW_FILE", "SCAN_NUMBER", "MODIFIED_SEQUENCE", "PRECURSOR_CHARGE"]
             self.metrics_val["Peptide"] = self.metadata["MODIFIED_SEQUENCE"].apply(lambda x: "_." + x + "._")
-            self.metrics_val["Proteins"] = self.metadata[
-                "MODIFIED_SEQUENCE"
-            ]  # we don't need the protein ID to get PSM / peptide results, fill with peptide sequence
+            self.metrics_val["Proteins"] = self.metadata["PROTEINS"]
 
         if "SCAN_EVENT_NUMBER" in self.metadata.columns:
             spec_id_cols.append("SCAN_EVENT_NUMBER")
@@ -348,8 +395,9 @@ def get_indices_below_fdr(self, feature_name: str, fdr_cutoff: float = 0.01) ->
 
         accepted_indices = scores_df.index[scores_df["fdr"] < fdr_cutoff]
         if len(accepted_indices) == 0:
-            logger.error(
-                f"Could not find any targets below {fdr_cutoff} out of {len(scores_df.index)} targets in total"
+            logger.warning(
+                f"Could not find any targets below {fdr_cutoff} out of {len(scores_df.index)} "
+                "targets in total. Retrying with higher FDR cutoff..."
             )
             return np.array([])
 
@@ -397,13 +445,15 @@ def _reorder_columns_for_percolator(self):
         new_columns = first_columns + sorted(mid_columns) + last_columns
         self.metrics_val = self.metrics_val[new_columns]
 
-    def calc(self):
+    def calc(self):  # noqa: C901
         """Adds percolator metadata and feature columns to metrics_val based on PSM metadata."""
         self.add_common_features()
         self.target_decoy_labels = self.metadata["REVERSE"].apply(Percolator.get_target_decoy_label).to_numpy()
         np.random.seed(1)
         # add Prosit or Andromeda features
         if self.input_type == "rescore":
+            # add additional features
+            self.add_additional_features()
             fragments_ratio = fr.FragmentsRatio(self.pred_intensities, self.true_intensities)
             fragments_ratio.calc(xl=self.xl)
             similarity = sim.SimilarityMetrics(self.pred_intensities, self.true_intensities, self.mz)
@@ -412,52 +462,61 @@ def calc(self):
             self.metrics_val = pd.concat(
                 [self.metrics_val, fragments_ratio.metrics_val, similarity.metrics_val], axis=1
             )
+            if self.neutral_loss_flag:
+                self.metrics_val["ANNOTATED_NL_COUNT"] = self.metadata["ANNOTATED_NL_COUNT"]
+                self.metrics_val["EXPECTED_NL_COUNT"] = self.metadata["EXPECTED_NL_COUNT"]
+                columns_to_remove = []
+                for col in self.metrics_val.columns:
+                    if "vs_predicted" in col:
+                        columns_to_remove.append(col)
+                self.metrics_val.drop(columns=columns_to_remove, inplace=True)
+            if self.drop_miss_cleavage_flag:
+                self.metrics_val.drop(columns=["missedCleavages", "KR"], inplace=True)
             if self.xl:
                 self.metrics_val["collision_energy_aligned"] = self.metadata["COLLISION_ENERGY"] / 100.0
             else:
                 lda_failed = False
                 idxs_below_lda_fdr = self.apply_lda_and_get_indices_below_fdr(fdr_cutoff=self.fdr_cutoff)
                 current_fdr = self.fdr_cutoff
-                while len(idxs_below_lda_fdr) == 0:
+                while len(idxs_below_lda_fdr) <= 500:
                     current_fdr += 0.01
                     idxs_below_lda_fdr = self.apply_lda_and_get_indices_below_fdr(fdr_cutoff=current_fdr)
                     if current_fdr >= 0.1:
                         lda_failed = True
                         break
+                if lda_failed:
+                    sampled_idxs = Percolator.sample_balanced_over_bins(
+                        self.metadata[["RETENTION_TIME", "PREDICTED_IRT"]]
+                    )
                 else:
-                    if lda_failed:
-                        sampled_idxs = Percolator.sample_balanced_over_bins(
-                            self.metadata[["RETENTION_TIME", "PREDICTED_IRT"]]
-                        )
-                    else:
-                        sampled_idxs = Percolator.sample_balanced_over_bins(
-                            self.metadata[["RETENTION_TIME", "PREDICTED_IRT"]].iloc[idxs_below_lda_fdr, :]
-                        )
-
-                    file_sample = self.metadata.iloc[sampled_idxs].sort_values("PREDICTED_IRT")
-                    aligned_predicted_rts = Percolator.get_aligned_predicted_retention_times(
-                        file_sample["RETENTION_TIME"],
-                        file_sample["PREDICTED_IRT"],
-                        self.metadata["PREDICTED_IRT"],
-                        self.regression_method,
+                    sampled_idxs = Percolator.sample_balanced_over_bins(
+                        self.metadata[["RETENTION_TIME", "PREDICTED_IRT"]].iloc[idxs_below_lda_fdr, :]
                     )
 
-                    self.metrics_val["RT"] = self.metadata["RETENTION_TIME"]
-                    self.metrics_val["pred_RT"] = self.metadata["PREDICTED_IRT"]
-                    self.metrics_val["iRT"] = aligned_predicted_rts
-                    self.metrics_val["collision_energy_aligned"] = self.metadata["COLLISION_ENERGY"] / 100.0
-                    self.metrics_val["abs_rt_diff"] = np.abs(self.metadata["RETENTION_TIME"] - aligned_predicted_rts)
-
-                    median_abs_error_lda_targets = np.median(self.metrics_val["abs_rt_diff"].iloc[idxs_below_lda_fdr])
-                    logger.info(
-                        "Median absolute error predicted vs observed retention time on targets < 1% FDR: "
-                        f"{median_abs_error_lda_targets}"
-                    )
-                    logger.debug(
-                        self.metrics_val[["RT", "pred_RT", "abs_rt_diff", "lda_scores"]].iloc[idxs_below_lda_fdr, :]
-                    )
+                file_sample = self.metadata.iloc[sampled_idxs].sort_values("PREDICTED_IRT")
+                aligned_predicted_rts = Percolator.get_aligned_predicted_retention_times(
+                    file_sample["RETENTION_TIME"],
+                    file_sample["PREDICTED_IRT"],
+                    self.metadata["PREDICTED_IRT"],
+                    self.regression_method,
+                )
+
+                self.metrics_val["RT"] = self.metadata["RETENTION_TIME"]
+                self.metrics_val["pred_RT"] = self.metadata["PREDICTED_IRT"]
+                self.metrics_val["iRT"] = aligned_predicted_rts
+                self.metrics_val["collision_energy_aligned"] = self.metadata["COLLISION_ENERGY"] / 100.0
+                self.metrics_val["abs_rt_diff"] = np.abs(self.metadata["RETENTION_TIME"] - aligned_predicted_rts)
+                if lda_failed:
+                    median_abs_error = np.median(self.metrics_val["abs_rt_diff"])
+                else:
+                    median_abs_error = np.median(self.metrics_val["abs_rt_diff"].iloc[idxs_below_lda_fdr])
+                logger.info(
+                    "Median absolute error predicted vs observed retention time on targets < 1% FDR: "
+                    f"{median_abs_error}"
+                )
 
         else:
+            self.add_additional_features()
             self.metrics_val["andromeda"] = self.metadata["SCORE"]
 
         self.add_percolator_metadata_columns()
@@ -497,6 +556,10 @@ def spline(knots: int, x: np.ndarray, y: np.ndarray):
     """Calculates spline fitting."""
     x_new = np.linspace(0, 1, knots + 2)[1:-1]
     q_knots = np.quantile(x, x_new)
+    if q_knots[0] == 0:
+        q_knots[0] += 1e-6
+    if q_knots[0] == q_knots[1]:
+        q_knots[1] += 1e-6
     t, c, k = interpolate.splrep(x, y, t=q_knots, s=2)
     yfit = interpolate.BSpline(t, c, k)(x)
     return yfit, t, c, k
diff --git a/spectrum_fundamentals/metrics/similarity.py b/spectrum_fundamentals/metrics/similarity.py
index 930df61..e637ccc 100644
--- a/spectrum_fundamentals/metrics/similarity.py
+++ b/spectrum_fundamentals/metrics/similarity.py
@@ -171,9 +171,9 @@ def spectral_entropy_similarity(
         :param predicted_intensities: predicted intensities, see observed_intensities for details, array of length 174
         :return: spectral entropy similarity values
         """
-        if type(observed_intensities) == scipy.sparse.csr_matrix:
+        if isinstance(observed_intensities, scipy.sparse.csr_matrix):
             observed_intensities = observed_intensities.toarray()
-        if type(predicted_intensities) == scipy.sparse.csr_matrix:
+        if isinstance(predicted_intensities, scipy.sparse.csr_matrix):
             predicted_intensities = predicted_intensities.toarray()
 
         entropies = []
@@ -481,9 +481,6 @@ def _calc_additional_metrics(
             true_intensities, pred_intensities, "max"
         )
         self.metrics_val[f"mse{key_suffix}"] = SimilarityMetrics.abs_diff(true_intensities, pred_intensities, "mse")
-        self.metrics_val[f"modified_cosine{key_suffix}"] = SimilarityMetrics.modified_cosine(
-            true_intensities, pred_intensities, self.mz, self.mz
-        )
 
         col_names_spectral_angle = [
             f"spectral_angle_{amount}_charge{key_suffix}" for amount in ["single", "double", "triple"]
@@ -539,3 +536,7 @@ def _calc_additional_metrics(
                 self.metrics_val[col_name_spearman_corr] = SimilarityMetrics.correlation(
                     true_intensities, pred_intensities, i + 1, "spearman"
                 )
+
+            self.metrics_val[f"modified_cosine{key_suffix}"] = SimilarityMetrics.modified_cosine(
+                true_intensities, pred_intensities, self.mz, self.mz
+            )
diff --git a/spectrum_fundamentals/mod_string.py b/spectrum_fundamentals/mod_string.py
index 03773f1..913b8e2 100644
--- a/spectrum_fundamentals/mod_string.py
+++ b/spectrum_fundamentals/mod_string.py
@@ -1,24 +1,15 @@
 import difflib
 import re
 from itertools import combinations, repeat
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Dict, List, Optional, Set, Tuple, Union
 
 import numpy as np
 import pandas as pd
 
-from .constants import (
-    MAXQUANT_VAR_MODS,
-    MOD_MASSES,
-    MOD_MASSES_SAGE,
-    MOD_NAMES,
-    MSFRAGGER_VAR_MODS,
-    OPENMS_VAR_MODS,
-    SPECTRONAUT_MODS,
-    XISEARCH_VAR_MODS,
-)
+from .constants import MOD_MASSES, MOD_NAMES, SPECTRONAUT_MODS, XISEARCH_VAR_MODS, OPENMS_VAR_MODS
 
 
-def sage_to_internal(sequences: List[str]) -> List[str]:
+def sage_to_internal(sequences: List[str], mods: Dict[str, str]) -> List[str]:
     """
     Convert mod string from sage to the internal format.
 
@@ -28,34 +19,50 @@ def sage_to_internal(sequences: List[str]) -> List[str]:
     modifications defined in the constants.
 
     :param sequences: A list of sequences with values inside square brackets.
+    :param mods: Dict with all Sage-specific and custom modifications
+    :raises AssertionError: if modifications in custom or internal format were provided in the wrong type.
     :return: A list of modified sequences with values converted to internal format.
     """
     # Define a regular expression pattern to match values within square brackets, like [+1.0] or [-2.0].
     pattern = r"[A-Z]?\[([\+\-]\d+\.\d+)\]-?"
 
+    # Define a function 'replace' that takes a regex match object.
     # Define a function 'replace' that takes a regex match object.
     def replace(match):
         # Extract the value inside the square brackets as a float.
-        value = float(match.group(1))
+        value = str(float(match.group(1)))
         key = match.string[match.start() : match.end()]
         if key.endswith("-"):
-            unimod_expression = f"{MOD_MASSES_SAGE.get(value, match.group(0))}-"
+            unimod_expression = f"{mods.get(value, match.group(0))}-"
+        # custom mods can be either the entire key or just the numeric value as string
+        elif key in mods.keys() or value in mods.keys():
+            key_pref = ""
+            if key[0].isalpha():
+                key_pref = key[0]
+            unimod_expression = f"{key_pref}{mods.get(value, match.group(0))}"
         elif key.startswith("C"):
-            unimod_expression = f"C{MOD_MASSES_SAGE.get(value, match.group(0))}"
+            unimod_expression = f"C{mods.get(value, match.group(0))}"
         elif key.startswith("K"):
-            unimod_expression = f"K{MOD_MASSES_SAGE.get(value, match.group(0))}"
+            unimod_expression = f"K{mods.get(value, match.group(0))}"
         elif key.startswith("M"):
-            unimod_expression = f"M{MOD_MASSES_SAGE.get(value, match.group(0))}"
-
-        # Check if the 'MOD_MASSES_SAGE' dictionary has a replacement value for the extracted value.
+            unimod_expression = f"M{mods.get(value, match.group(0))}"
+        else:
+            unimod_expression = match.group(0)
+        # Check if the 'mods' dictionary has a replacement value for the extracted value.
         # If it does, use the replacement value; otherwise, use the original value from the match.
         return unimod_expression
 
     # Create an empty list 'modified_strings' to store the modified sequences.
     modified_strings = []
 
+    if not all(isinstance(val, str) for val in mods.values()) or not all(
+        isinstance(key, (str, float)) for key in mods.keys()
+    ):
+        raise AssertionError("All custom modifications entries must have keys of type str and values of type str.")
+
     # Iterate through the input 'sequences'.
     for string in sequences:
+
         # Use 're.sub' to search and replace values within square brackets in the 'string' using the 'replace' function.
         modified_string = re.sub(pattern, replace, string)
 
@@ -130,39 +137,23 @@ def internal_to_spectronaut(sequences: Union[np.ndarray, pd.Series, List[str]])
     return [regex.sub(lambda mo: SPECTRONAUT_MODS[mo.string[mo.start() : mo.end()]], seq) for seq in sequences]
 
 
-def maxquant_to_internal(
-    sequences: Union[np.ndarray, pd.Series, List[str]], fixed_mods: Optional[Dict[str, str]] = None
-) -> List[str]:
+def maxquant_to_internal(sequences: Union[np.ndarray, pd.Series, List[str]], mods: Dict[str, str]) -> List[str]:
     """
     Function to translate a MaxQuant modstring to the Prosit format.
 
     :param sequences: List[str] of sequences
-    :param fixed_mods: Optional dictionary of modifications with key aa and value mod, e.g. 'M': 'M(UNIMOD:35)'.
-        Fixed modifications must be included in the variable modificatons dictionary.
-        By default, i.e. if nothing is supplied to fixed_mods, carbamidomethylation on cystein will be included
-        in the fixed modifications. If you want to have no fixed modifictions at all, supply fixed_mods={}
-    :raises AssertionError: if illegal modification was provided in the fixed_mods dictionary.
+    :param mods: Dictionary of modifications with optional fixed mods (key aa and value mod, e.g. 'M[147]': '[UNIMOD:35]').
+        custom variable modifications and standard MAXQUANT var mods. Custom static mods are not visible in the mod string,
+        therefore input needs to change to key = aa and value aa and unimod identifier.
+    :raises AssertionError: if illegal modification was provided in the fixed_mods dictionary or custom mods in illegal type format.
     :return: a list of modified sequences
     """
-    if fixed_mods is None:
-        fixed_mods = {"C": "C[UNIMOD:4]"}
-    err_msg = f"Provided illegal fixed mod, supported modifications are {set(MAXQUANT_VAR_MODS.values())}."
-    assert all(x in MAXQUANT_VAR_MODS.values() for x in fixed_mods.values()), err_msg
+    if not all(isinstance(val, str) for val in mods.values()) or not all(
+        isinstance(key, (str, float)) for key in mods.keys()
+    ):
+        raise AssertionError("All custom modifications entries must have keys of type str and values of type str.")
 
-    replacements = {**MAXQUANT_VAR_MODS, **fixed_mods}
-
-    def custom_regex_escape(key: str) -> str:
-        """
-        Subfunction to escape only normal brackets in the modstring.
-
-        :param key: The match to escape
-        :return: match with escaped special characters
-        """
-        for k, v in {"(": r"\(", ")": r"\)"}.items():
-            key = key.replace(k, v)
-        return key
-
-    regex = re.compile("|".join(map(custom_regex_escape, replacements.keys())))
+    regex = re.compile("|".join(map(custom_regex_escape, mods.keys())))
 
     def find_replacement(match: re.Match) -> str:
         """
@@ -178,56 +169,24 @@ def find_replacement(match: re.Match) -> str:
             else:
                 key = f"{key}$"
 
-        return replacements[key]
+        value = mods[key]
+        if key[0].isalpha() and not value[0].isalpha():
+            value = f"{key[0]}{value}"
+        return value
 
-    return [regex.sub(find_replacement, seq).replace("_", "") for seq in sequences]
+    return [regex.sub(lambda match: find_replacement(match), seq).replace("_", "") for seq in sequences]
 
 
-def msfragger_to_internal(
-    sequences: Union[np.ndarray, pd.Series, List[str]], fixed_mods: Optional[Dict[str, str]] = None
-) -> List[str]:
+def msfragger_to_internal(sequences: Union[np.ndarray, pd.Series, List[str]], mods: Dict[str, str]) -> List[str]:
     """
     Function to translate a MSFragger modstring to the Prosit format.
 
     :param sequences: List[str] of sequences
-    :param fixed_mods: Optional dictionary of modifications with key aa and value mod, e.g. 'M[147]': 'M(UNIMOD:35)'.
-        Fixed modifications must be included in the variable modificatons dictionary.
-        By default, i.e. if nothing is supplied to fixed_mods, carbamidomethylation on cystein will be included
-        in the fixed modifications. If you want to have no fixed modifictions at all, supply fixed_mods={}
-    :raises AssertionError: if illegal modification was provided in the fixed_mods dictionary.
+    :param mods: Dictionary of modifications with optional fixed mods (key aa and value mod, e.g. 'M[147]': '[UNIMOD:35]').
+        custom static and variable modifications and in case of MSFragger also standard static mods
     :return: a list of modified sequences
     """
-    if fixed_mods is None:
-        fixed_mods = {"C": "C[UNIMOD:4]"}
-    err_msg = f"Provided illegal fixed mod, supported modifications are {set(MSFRAGGER_VAR_MODS.values())}."
-    assert all(x in MSFRAGGER_VAR_MODS.values() for x in fixed_mods.values()), err_msg
-
-    replacements = {**MSFRAGGER_VAR_MODS, **fixed_mods}
-
-    def custom_regex_escape(key: str) -> str:
-        """
-        Subfunction to escape only normal brackets in the modstring.
-
-        :param key: The match to escape
-        :return: match with escaped special characters
-        """
-        for k, v in {"[": r"\[", "]": r"\]"}.items():
-            key = key.replace(k, v)
-        return key
-
-    def find_replacement(match: re.Match) -> str:
-        """
-        Subfunction to find the corresponding substitution for a match.
-
-        :param match: an re.Match object found by re.sub
-        :return: substitution string for the given match
-        """
-        key = match.string[match.start() : match.end()]
-        return replacements[key]
-
-    regex = re.compile("|".join(map(custom_regex_escape, replacements.keys())))
-
-    return [regex.sub(find_replacement, seq) for seq in sequences]
+    return _to_internal(sequences=sequences, mods=mods)
 
 def openms_to_internal(sequences: List[str], fixed_mods: Optional[Dict[str, str]] = None) -> List[str]:
     """
@@ -286,20 +245,56 @@ def internal_without_mods(sequences: List[str]) -> List[str]:
     return [re.sub(regex, "", seq) for seq in sequences]
 
 
-def internal_to_mod_mass(
-    sequences: List[str],
-) -> List[str]:
+def internal_to_mod_mass(sequences: List[str], custom_mods: Optional[Dict[str, float]] = None) -> List[str]:
     """
     Function to exchange the internal mod identifiers with the masses of the specific modifiction.
 
     :param sequences: List[str] of sequences
+    :param custom_mods: custom mods with the identifier (=key), respespective unimod identifier and mass (value)
     :return: List[str] of modified sequences
     """
-    regex = re.compile("(%s)" % "|".join(map(re.escape, MOD_MASSES.keys())))
-    replacement_func = lambda match: f"[+{MOD_MASSES[match.string[match.start():match.end()]]}]"
+    mod_masses = MOD_MASSES | (custom_mods or {})
+
+    regex = re.compile("(%s)" % "|".join(map(re.escape, mod_masses.keys())))
+    replacement_func = lambda match: f"[+{mod_masses[match.string[match.start():match.end()]]}]"
     return [regex.sub(replacement_func, seq) for seq in sequences]
 
 
+def internal_to_msp(
+    sequences: Union[List[str], pd.Series],
+    mods: Dict[str, str],
+) -> List[Tuple[str, str]]:
+    """
+    Function to translate an internal modstring to modstring and Mods for MSP format.
+
+    :param sequences: sequences to translate
+    :param mods: dictionary mapping from internal unimod format (keys) to MSP format (values).
+    :return: a tuple for each sequence, containing (Mods, mod_string) for the MSP format
+    """
+    ret_vals = []
+    p = re.compile("|".join(mods.keys()))
+    for seq in sequences:
+        offset = 0
+        mod_list = []
+        matches = p.finditer(seq)
+        for match in matches:
+            replacement = mods[re.escape(match.group())]
+            start, end = match.span()
+            actual_start = start - offset
+            mod_list.append((actual_start, replacement))
+
+            offset += end - start - 1
+
+        mod_string = "; ".join([f"{mod[2:]}@{mod[0]}{pos}" for pos, mod in mod_list])
+        n_mods = len(mod_list)
+        if n_mods > 0:
+            mods_field = f"{n_mods}/{'/'.join([f'{pos},{mod}' for pos, mod in mod_list])}"
+        else:
+            mods_field = "0"
+        ret_vals.append((mods_field, mod_string))
+    return ret_vals
+
+
 def internal_to_mod_names(
     sequences: List[str],
 ) -> List[Tuple[str, str]]:
@@ -361,10 +356,17 @@ def split_modstring(sequence: str, r_pattern):
         # Ugly and fast fix for reading modifications as is from maxquant we should reconsider how to fix it.
         # sequence = sequence.replace('M(ox)','M(U:35)')
         # sequence = sequence.replace('C','C(U:4)')
+        val = max(alphabet.values()) + 1
         split_seq = r_pattern.findall(sequence)
         if "".join(split_seq) == sequence:
             if translate:
-                return [alphabet[aa] for aa in split_seq]
+                results = []
+                for aa in split_seq:
+                    if aa not in alphabet:  # does not exist
+                        alphabet[aa] = val
+                        val += 1
+                    results.append(alphabet[aa])
+                return results
             else:
                 return split_seq
         elif filter:
@@ -377,29 +379,52 @@ def split_modstring(sequence: str, r_pattern):
                 f"The element(s) [{not_parsable_elements}] " f"in the sequence [{sequence}] could not be parsed"
             )
 
-    pattern = sorted(alphabet, key=len, reverse=True)
+    unimod_pattern = r"[A-Z]\[UNIMOD:\d+\]"
+    alphabet_pattern = [re.escape(i) for i in sorted(alphabet, key=len, reverse=True)]
 
-    pattern = [re.escape(i) for i in pattern]
+    pattern = [unimod_pattern] + alphabet_pattern
     regex_pattern = re.compile("|".join(pattern))
     return map(split_modstring, sequences, repeat(regex_pattern))
 
 
-def add_permutations(modified_sequence: str, unimod_id: int, residues: List[str]):
+def get_all_tokens(sequences: List[str]) -> Set[str]:
+    """Parse given sequences in UNIMOD ProForma standard into a set of all tokens."""
+    pattern = r"[ACDEFGHIKLMNPQRSTVWY](\[UNIMOD:\d+\])?"
+    tokens = set()
+    for seq in sequences:
+        tokens |= {match.group() for match in re.finditer(pattern, seq)}
+    return tokens
+
+
+def add_permutations(
+    modified_sequence: str, unimod_id: int, residues: List[str], allow_one_less_modification: bool = False
+):
     """
     Generate different peptide sequences with moving the modification to all possible residues.
 
     :param modified_sequence: Peptide sequence
     :param unimod_id: modification unimod id to be used for generating different permutations.
     :param residues: possible amino acids where this mod can exist
+    :param allow_one_less_modification: Flag to indicate if permutations with one less modification should be generated to check
+        whether the modification mass was mistakenly picked as the monoisotopic peak. Mainly used for Citrullination.
     :return: list of possible sequence permutations
     """
-    sequence = modified_sequence.replace("[UNIMOD:" + str(unimod_id) + "]", "")
-    modifications = len(re.findall("UNIMOD:" + str(unimod_id), modified_sequence))
+    modified_sequence = modified_sequence.replace("UNIMOD", "unimod")
+    sequence = modified_sequence.replace("[unimod:" + str(unimod_id) + "]", "")
+    modifications = len(re.findall("unimod:" + str(unimod_id), modified_sequence))
     if modifications == 0:
-        return modified_sequence
+        modified_sequence = modified_sequence.replace("unimod", "UNIMOD")
+        return [modified_sequence]
     possible_positions = [i for i, ltr in enumerate(sequence) if ltr in residues]
     possible_positions.sort(reverse=True)
     all_combinations = [list(each_permutation) for each_permutation in combinations(possible_positions, modifications)]
+
+    if allow_one_less_modification:
+        all_combinations_1 = [
+            list(each_permutation) for each_permutation in combinations(possible_positions, modifications - 1)
+        ]
+        all_combinations = all_combinations + all_combinations_1
+
     modified_sequences_comb = []
     for comb in all_combinations:
         modified_sequence = sequence
@@ -407,6 +432,7 @@ def add_permutations(modified_sequence: str, unimod_id: int, residues: List[str]
             modified_sequence = (
                 modified_sequence[: index + 1] + "[unimod:" + str(unimod_id) + "]" + modified_sequence[index + 1 :]
             )
+        modified_sequence = modified_sequence.replace("unimod", "UNIMOD")
         modified_sequences_comb.append(modified_sequence)
     return modified_sequences_comb
 
@@ -473,3 +499,55 @@ def get_mods_list(mods_variable: str, mods_fixed: str):
         return mods_variable.split(";")
     else:
         return mods_variable.split(";") + mods_fixed.split(";")
+
+
+def custom_regex_escape(key: str) -> str:
+    """
+    Subfunction to escape normal, square brackets and the plus-sign in the modstring.
+
+    :param key: The match to escape
+    :return: match with escaped special characters
+    """
+    for k, v in {"(": r"\(", ")": r"\)", "[": r"\[", "]": r"\]", "+": r"\+", "-": r"\-"}.items():
+        key = key.replace(k, v)
+    return key
+
+
+def custom_to_internal(sequences: Union[np.ndarray, pd.Series, List[str]], mods: Dict[str, str]) -> List[str]:
+    """
+    Function to translate custom modstrings to the Prosit format.
+
+    :param sequences: List[str] of sequences
+    :param mods: Dictionary of modifications with optional fixed mods (key aa and value mod, e.g. 'M[147]': '[UNIMOD:35]').
+        custom static and variable modifications and in case of MSFragger also standard static mods
+    :return: a list of modified sequences
+    """
+    return _to_internal(sequences=sequences, mods=mods)
+
+
+def _to_internal(sequences: Union[np.ndarray, pd.Series, List[str]], mods: Dict[str, str]) -> List[str]:
+    """
+    Function to translate a modstring to the internal Prosit format.
+
+    :param sequences: List[str] of sequences
+    :param mods: Dictionary of modifications with optional fixed mods (key aa and value mod, e.g. 'M[147]': '[UNIMOD:35]').
+        custom static and variable modifications and in case of MSFragger also standard static mods
+    :return: a list of modified sequences
+    """
+
+    def find_replacement(match: re.Match) -> str:
+        """
+        Subfunction to find the corresponding substitution for a match.
+
+        :param match: an re.Match object found by re.sub
+        :return: substitution string for the given match
+        """
+        key = match.string[match.start() : match.end()]
+        value = mods[key]
+        if key[0].isalpha() and key[0].isupper() and not value[0].isalpha():
+            value = f"{key[0]}{value}"
+        return value
+
+    regex = re.compile("|".join(map(custom_regex_escape, mods.keys())))
+
+    return [regex.sub(lambda match: find_replacement(match), seq) for seq in sequences]
diff --git a/tests/unit_tests/data/annotation_xl_cl_output.json b/tests/unit_tests/data/annotation_xl_cl_output.json
index 049d8e1..5cc3a99 100644
--- a/tests/unit_tests/data/annotation_xl_cl_output.json
+++ b/tests/unit_tests/data/annotation_xl_cl_output.json
@@ -1,6 +1,6 @@
-[
-    {
-        "INTENSITIES_A": [
+{
+    "INTENSITIES_A": {
+        "0": [
             1.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0,
             0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0,
             -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0,
@@ -33,11 +33,14 @@
             -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
             -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0
         ],
-        "INTENSITIES_B": [
-            0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0,
-            0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0,
-            -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 1.0, 0.0,
-            -1.0, 0.0, 0.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
+        "1": [
+            0.5336033987, 0.0, -1.0, 0.0, 0.0, -1.0, 0.4464429494, 0.0, -1.0,
+            0.2501760443, 0.0, -1.0, 0.6483555549, 0.051478993, -1.0,
+            0.0193635044, 0.0, -1.0, 0.1885797428, 0.1646983684, -1.0,
+            0.0301492272, 0.0, -1.0, 0.04490012, 0.0580133805, -1.0, 0.0, 0.0,
+            -1.0, 0.0942211574, 0.8777324399, -1.0, 0.0085736376, 0.0, -1.0,
+            0.0149206348, 1.0, -1.0, 0.0087054536, 0.0, -1.0, -1.0, -1.0, -1.0,
+            -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
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diff --git a/tests/unit_tests/data/spectrum_output.csv b/tests/unit_tests/data/spectrum_output.csv
index 4c351e0..e263c56 100644
--- a/tests/unit_tests/data/spectrum_output.csv
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diff --git a/tests/unit_tests/data/tmt_spectrum_input.json b/tests/unit_tests/data/tmt_spectrum_input.json
new file mode 100644
index 0000000..5ce0851
--- /dev/null
+++ b/tests/unit_tests/data/tmt_spectrum_input.json
@@ -0,0 +1,1875 @@
+{
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+        "2": "[UNIMOD:737]-AAAAPNK[UNIMOD:737]",
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+        "4": "[UNIMOD:737]-AAADFATHGK[UNIMOD:737]"
+    },
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+    "MASS_ANALYZER": {
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diff --git a/tests/unit_tests/data/tmt_spectrum_output.json b/tests/unit_tests/data/tmt_spectrum_output.json
new file mode 100644
index 0000000..7d99d64
--- /dev/null
+++ b/tests/unit_tests/data/tmt_spectrum_output.json
@@ -0,0 +1,245 @@
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+    },
+    "CALCULATED_MASS": {
+        "0": 1384.81018667,
+        "1": 1027.64535267,
+        "2": 1099.67553867,
+        "3": 1957.03579667,
+        "4": 1445.80325967
+    },
+    "removed_peaks": { "0": 0, "1": 0, "2": 1, "3": 0, "4": 0 },
+    "ANNOTATED_NL_COUNT": { "0": 0, "1": 0, "2": 0, "3": 0, "4": 0 },
+    "EXPECTED_NL_COUNT": { "0": 0, "1": 0, "2": 0, "3": 0, "4": 0 }
+}
diff --git a/tests/unit_tests/test_annotation.py b/tests/unit_tests/test_annotation.py
index 5722f37..bbf8ada 100644
--- a/tests/unit_tests/test_annotation.py
+++ b/tests/unit_tests/test_annotation.py
@@ -30,6 +30,26 @@ def test_annotate_spectra(self):
         result = annotation.annotate_spectra(spectrum_input)
         pd.testing.assert_frame_equal(expected_result, result)
 
+    def test_annotate_spectra_with_custom_mods(self):
+        """Test annotate spectra."""
+        spectrum_input = pd.read_csv(
+            Path(__file__).parent / "data/spectrum_input.csv",
+            index_col=0,
+            converters={"INTENSITIES": literal_eval, "MZ": literal_eval},
+        )
+
+        expected_result = pd.read_csv(
+            Path(__file__).parent / "data/spectrum_output.csv",
+            index_col=0,
+            converters={"INTENSITIES": literal_eval, "MZ": literal_eval},
+        )
+        spectrum_input["INTENSITIES"] = spectrum_input["INTENSITIES"].map(lambda intensities: np.array(intensities))
+        spectrum_input["MZ"] = spectrum_input["MZ"].map(lambda mz: np.array(mz))
+        custom_mods = {"[UNIMOD:4]": 57.0215, "[UNIMOD:35]": 15.99}
+
+        result = annotation.annotate_spectra(un_annot_spectra=spectrum_input, custom_mods=custom_mods)
+        pd.testing.assert_frame_equal(expected_result, result)
+
     def test_annotate_spectra_noncl_xl(self):
         """Test annotate spectra non cleavable crosslinked peptides."""
         spectrum_input = pd.read_json(
@@ -53,6 +73,22 @@ def test_annotate_spectra_cl_xl(self):
         result = annotation.annotate_spectra(spectrum_input)
         pd.testing.assert_frame_equal(expected_result, result)
 
+    def test_annotate_spectra_tmt(self):
+        """Test annotate TMT spectra."""
+        spectrum_input = pd.read_json(
+            Path(__file__).parent / "data/tmt_spectrum_input.json",
+            # converters={"INTENSITIES": literal_eval, "MZ": literal_eval},
+        )
+        expected_result = pd.read_json(
+            Path(__file__).parent / "data/tmt_spectrum_output.json",
+        )
+
+        spectrum_input["INTENSITIES"] = spectrum_input["INTENSITIES"].map(lambda intensities: np.array(intensities))
+        spectrum_input["MZ"] = spectrum_input["MZ"].map(lambda mz: np.array(mz))
+
+        result = annotation.annotate_spectra(spectrum_input)
+        pd.testing.assert_frame_equal(expected_result, result)
+
     def test_handle_multiple_matches(self):
         """Test handle_multiple_matches function."""
         # Example input data with multiple matches. They don't make biological sense but it tests the mathematical correctness.
diff --git a/tests/unit_tests/test_constants.py b/tests/unit_tests/test_constants.py
deleted file mode 100644
index e69de29..0000000
diff --git a/tests/unit_tests/test_fragments.py b/tests/unit_tests/test_fragments.py
index b45e5b2..de62a9a 100644
--- a/tests/unit_tests/test_fragments.py
+++ b/tests/unit_tests/test_fragments.py
@@ -4,183 +4,224 @@
 
 from numpy.testing import assert_almost_equal
 
+import spectrum_fundamentals.constants as c
 import spectrum_fundamentals.fragments as fragments
 
 
-class TestGetModifications:
-    """Class to test get modifications."""
-
-    def test_get_modifications(self):
-        """Test get_modifications."""
-        assert fragments._get_modifications("ABC") == {}
-
-    def test_get_modifications_carbamidomethylation(self):
-        """Test get_modifications."""
-        assert fragments._get_modifications("ABC[UNIMOD:4]") == {2: 57.021464}
-
-    def test_get_modifications_tmt_tag(self):
-        """Test get_modifications."""
-        assert fragments._get_modifications("[UNIMOD:737]-ABC[UNIMOD:4]") == {-2: 229.162932, 2: 57.021464}
-
-    def test_get_modifications_tmtpro_tag(self):
-        """Test get_modifications."""
-        assert fragments._get_modifications("[UNIMOD:2016]-ABC[UNIMOD:4]") == {-2: 304.207146, 2: 57.021464}
-
-
-class TestComputeMasses(unittest.TestCase):
-    """Class to test compute ion and peptide masses."""
-
-    def test_compute_ion_masses(self):
-        """
-        Test compute ion masses.
-
-        >>> from pyteomics import mass
-        >>> mass.calculate_mass(sequence='AD', ion_type='b', charge=1)
-        """
-        masses = fragments.compute_ion_masses([1, 3, 4] + [0] * 27, [1, 0, 0, 0, 0, 0])  # peptide = ADE, charge = 1
-        assert_almost_equal(masses[0], 148.06044, decimal=5)  # y1 E.-
-        assert_almost_equal(masses[1], -1.0, decimal=5)  # y1;2+: n.a.
-        assert_almost_equal(masses[3], 72.04439, decimal=5)  # b1: -.A
-        assert_almost_equal(masses[6], 263.08738, decimal=5)  # y2 DE.-
-        assert_almost_equal(masses[9], 187.07133, decimal=5)  # b2: -.AD
-
-    def test_compute_ion_masses_tmtpro(self):
-        """
-        Test compute ion masses.
-
-        >>> from pyteomics import mass
-        >>> mass.calculate_mass(sequence='AD', ion_type='b', charge=1)
-        """
-        masses = fragments.compute_ion_masses(
-            [1, 3, 4] + [0] * 27, [1, 0, 0, 0, 0, 0], "tmtpro"
-        )  # peptide = [UNIMOD:2016]ADE, charge = 1
-        assert_almost_equal(masses[0], 148.06044, decimal=5)  # y1 E.-
-        assert_almost_equal(masses[1], -1.0, decimal=5)  # y1;2+: n.a.
-        assert_almost_equal(masses[3], 72.04439 + 304.207146, decimal=5)  # b1: -.A
-        assert_almost_equal(masses[6], 263.08738, decimal=5)  # y2 DE.-
-        self.assertAlmostEqual(masses[9], 187.07133 + 304.207146, places=5)  # b2: -.AD
-
-    def test_compute_peptide_masses(self):
-        """Test computation of peptide masses with valid input."""
-        seq = "SEQUENC[UNIMOD:4]E"
-        self.assertEqual(fragments.compute_peptide_mass(seq), 1045.2561556699998)
-
-    def test_compute_peptide_masses_tmtpro(self):
-        """Test computation of peptide masses with valid input and tmt tag."""
-        seq = "[UNIMOD:737]-SEQUENC[UNIMOD:4]E"
-        self.assertEqual(fragments.compute_peptide_mass(seq), 1274.41908767)
-
-    def test_compute_peptide_masses_with_invalid_syntax(self):
-        """Negative testing of comuptation of peptide mass with unsupported syntax of mod string."""
-        seq = "SEQUEM(Ox.)CE"
-        self.assertRaises(KeyError, fragments.compute_peptide_mass, seq)
-
-    def test_compute_peptide_masses_with_invalid_mod(self):
-        """Negative testing of computation of peptide mass with unknown modification in mod string."""
-        seq = "SEQUENC[UNIMOD:0]E"
-        self.assertRaises(KeyError, fragments.compute_peptide_mass, seq)
-
-
-class TestMassTolerances(unittest.TestCase):
-    """Testing the mass tolerance calculations in various scenarios."""
-
-    def test_mass_tol_with_ppm(self):
-        """Test get_min_max_mass with a user defined ppm measure."""
-        window = fragments.get_min_max_mass(
-            mass_analyzer="FTMS", mass=10.0, mass_tolerance=15, unit_mass_tolerance="ppm"
-        )
-        self.assertEqual(window, (9.99985, 10.00015))
-
-    def test_mass_tol_with_da(self):
-        """Test get_min_max_mass with a user defined da measure."""
-        window = fragments.get_min_max_mass(
-            mass_analyzer="FTMS", mass=10.0, mass_tolerance=0.3, unit_mass_tolerance="da"
-        )
-        self.assertEqual(window, (9.7, 10.3))
-
-    def test_mass_tol_with_defaults(self):
-        """Test get_min_max_mass with mass analyzer defaults."""
-        window_ftms = fragments.get_min_max_mass(mass_analyzer="FTMS", mass=10.0)
-        window_itms = fragments.get_min_max_mass(mass_analyzer="ITMS", mass=10.0)
-        window_tof = fragments.get_min_max_mass(mass_analyzer="TOF", mass=10.0)
-
-        self.assertEqual(window_ftms, (9.9998, 10.0002))
-        self.assertEqual(window_tof, (9.9996, 10.0004))
-        self.assertEqual(window_itms, (9.65, 10.35))
-
-
 class TestInitializePeaks(unittest.TestCase):
     """Class to test initialize_peaks function."""
 
-    def test_initialize_peaks(self):
-        """Test initialize_peaks with basic input."""
-        fragments_input = {"sequence": "AAAA", "mass_analyzer": "FTMS", "charge": 3, "noncl_xl": False}
+    def _test_outputs(self, expected_input_file: Path, fragmentation_method: str):
 
-        with open(Path(__file__).parent / "data/fragments_meta_data.json") as file:
+        with open(expected_input_file) as file:
             expected_list_out = json.load(file)
-        expected_tmt_nt_term = 1
-        expected_peptide_sequence = "AAAA"
-        expected_mass_s = 302.15902
 
-        actual_list_out, actual_tmt_n_term, actual_peptide_sequence, actual_calc_mass_s = fragments.initialize_peaks(
-            **fragments_input
+        expected_tmt_nt_term = 1
+        expected_peptide_sequence = "PEPTIDE"
+        expected_mass_s = 799.3599646700001
+        expected_nl_annotated = 0
+
+        actual_list_out, actual_tmt_n_term, actual_peptide_sequence, actual_calc_mass_s, actual_nl_annotated = (
+            fragments.initialize_peaks(
+                sequence="PEPTIDE",
+                mass_analyzer="FTMS",
+                charge=3,
+                fragmentation_method=fragmentation_method,
+            )
         )
 
         self.assertEqual(actual_list_out, expected_list_out)
         self.assertEqual(actual_tmt_n_term, expected_tmt_nt_term)
         self.assertEqual(actual_peptide_sequence, expected_peptide_sequence)
         assert_almost_equal(actual_calc_mass_s, expected_mass_s, decimal=5)
+        self.assertEqual(actual_nl_annotated, expected_nl_annotated)
 
-    def test_initialize_peaks_non_cl_xl(self):
-        """Test initialize_peaks_xl with basic input for non-cleavable crosslinked peptides."""
-        initialize_peaks_xl_input = {
-            "sequence": "AKC",
-            "mass_analyzer": "FTMS",
-            "crosslinker_position": 2,
-            "crosslinker_type": "BS3",
-            "sequence_beta": "AKA",
-        }
+    def test_initialize_peaks_hcd_cid(self):
+        """Test initialize_peaks for HCD / CID input."""
+        self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_hcd_cid.json", "HCD")
+        self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_hcd_cid.json", "CID")
+
+    def test_initialize_peaks_etd_ecd(self):
+        """Test initialize_peaks for ETD / ECD input."""
+        self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_etd_ecd.json", "ETD")
+        self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_etd_ecd.json", "ECD")
+
+    def test_initialize_peaks_ethcd_etcid(self):
+        """Test initialize_peaks for ETCID / ETHCD input."""
+        self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_ethcd_etcid.json", "ETHCD")
+        self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_ethcd_etcid.json", "ETCID")
+
+    def test_initialize_peaks_uvpd(self):
+        """Test initialize_peaks with basic input, but for all six ion types for UVPD."""
+        self._test_outputs(Path(__file__).parent / "data/fragments_meta_data_uvpd.json", "UVPD")
+
+    def _test_xl_outputs(self, expected_input_file: Path, **fragments_input):
+
+        with open(expected_input_file) as file:
+            expected_list_out = json.load(file)
 
-        with open(Path(__file__).parent / "data/fragments_meta_data_non_cl_xl.json") as file:
-            expected_fragments_meta_data = json.load(file)
         expected_tmt_nt_term = 1
-        expected_peptide_sequence = "AKC"
-        expected_mass = 320.15182
+        expected_peptide_sequence = "PEKTIDE"
+        expected_mass = 830.40216367
 
         (
             actual_fragments_meta_data,
             actual_tmt_n_term,
             actual_peptide_sequence,
             actual_mass,
-        ) = fragments.initialize_peaks_xl(**initialize_peaks_xl_input)
-        self.assertEqual(actual_fragments_meta_data, expected_fragments_meta_data)
+        ) = fragments.initialize_peaks_xl(**fragments_input)
+
+        self.assertEqual(actual_fragments_meta_data, expected_list_out)
         self.assertEqual(actual_tmt_n_term, expected_tmt_nt_term)
         self.assertEqual(actual_peptide_sequence, expected_peptide_sequence)
         assert_almost_equal(actual_mass, expected_mass, decimal=5)
 
+    def test_initialize_peaks_non_cl_xl(self):
+        """Test initialize_peaks_xl with basic input for non-cleavable crosslinked peptides."""
+        initialize_peaks_xl_input = {
+            "sequence": "PEK[UNIMOD:1898]TIDE",
+            "mass_analyzer": "FTMS",
+            "crosslinker_position": 3,
+            "crosslinker_type": "BS3",
+            "sequence_beta": "AK[UNIMOD:1898]AT",
+        }
+        self._test_xl_outputs(
+            Path(__file__).parent / "data/fragments_meta_data_non_cl_xl.json", **initialize_peaks_xl_input
+        )
+
     def test_initialize_peaks_cl_xl(self):
         """Test initialize_peaks_xl with basic input for cleavable crosslinked peptides."""
         initialize_peaks_xl_input = {
-            "sequence": "AKC",
+            "sequence": "PEK[UNIMOD:1896]TIDE",
             "mass_analyzer": "FTMS",
-            "crosslinker_position": 2,
+            "crosslinker_position": 3,
             "crosslinker_type": "DSSO",
-            "sequence_beta": "AKA",
         }
+        self._test_xl_outputs(
+            Path(__file__).parent / "data/fragments_meta_data_cl_xl.json", **initialize_peaks_xl_input
+        )
 
-        with open(Path(__file__).parent / "data/fragments_meta_data_cl_xl.json") as file:
-            expected_fragments_meta_data = json.load(file)
-        expected_tmt_nt_term = 1
-        expected_peptide_sequence = "AKC"
-        expected_mass = 320.15182
 
-        (
-            actual_fragments_meta_data,
-            actual_tmt_n_term,
-            actual_peptide_sequence,
-            actual_mass,
-        ) = fragments.initialize_peaks_xl(**initialize_peaks_xl_input)
-        self.assertEqual(actual_fragments_meta_data, expected_fragments_meta_data)
-        self.assertEqual(actual_tmt_n_term, expected_tmt_nt_term)
-        self.assertEqual(actual_peptide_sequence, expected_peptide_sequence)
-        assert_almost_equal(actual_mass, expected_mass, decimal=5)
+class TestFragmentationMethod(unittest.TestCase):
+    """Class to test the retrieving of the IonTypes."""
+
+    def test_get_ion_types_hcd(self):
+        """Test retrieving ion types for HCD."""
+        assert fragments.retrieve_ion_types("HCD") == ["y", "b"]
+
+    def test_get_ion_types_etd(self):
+        """Test retrieving ion types for ETD."""
+        assert fragments.retrieve_ion_types("ETD") == ["z_r", "c"]
+
+    def test_get_ion_types_etcid(self):
+        """Test retrieving ion types for ETCID."""
+        assert fragments.retrieve_ion_types("ETCID") == ["y", "b", "z_r", "c"]
+
+    def test_get_ion_types_lower_case(self):
+        """Test lower case fragmentation method."""
+        assert fragments.retrieve_ion_types("uvpd") == ["x", "a", "y", "b", "z", "c"]
+
+    def test_invalid_fragmentation_method(self):
+        """Test if error is raised for invalid fragmentation method."""
+        self.assertRaises(ValueError, fragments.retrieve_ion_types, "XYZ")
+
+
+class TestFragmentationMethodForPeakInitialization(unittest.TestCase):
+    """Class to test the retrieving of the IonTypes for peak initialization."""
+
+    def test_get_ion_types_hcd(self):
+        """Test retrieving ion types for HCD."""
+        assert fragments.retrieve_ion_types_for_peak_initialization("HCD") == ["y", "b"]
+
+    def test_get_ion_types_etd(self):
+        """Test retrieving ion types for ETD."""
+        assert fragments.retrieve_ion_types_for_peak_initialization("ETD") == ["z_r", "c"]
+
+    def test_get_ion_types_etcid(self):
+        """Test retrieving ion types for ETCID."""
+        assert fragments.retrieve_ion_types_for_peak_initialization("ETCID") == ["y", "z_r", "b", "c"]
+
+    def test_get_ion_types_lower_case(self):
+        """Test lower case fragmentation method."""
+        assert fragments.retrieve_ion_types_for_peak_initialization("uvpd") == ["x", "y", "z", "a", "b", "c"]
+
+    def test_invalid_fragmentation_method(self):
+        """Test if error is raised for invalid fragmentation method."""
+        self.assertRaises(ValueError, fragments.retrieve_ion_types_for_peak_initialization, "XYZ")
+
+
+class TestFragmentIonAnnotation(unittest.TestCase):
+    """Tests for fragment ion annotation generation."""
+
+    def test_generate_fragment_ion_types(self):
+        """Test if output ordering is valid."""
+        for ion_types in [["y", "b"], ["b", "y"], ["y", "b", "x", "a"]]:
+            order = ("position", "ion_type", "charge")
+            annotations = [
+                (ion_type, pos, charge) for pos in c.POSITIONS for ion_type in ion_types for charge in c.CHARGES
+            ]
+            with self.subTest(order=order, ion_types=ion_types):
+                self.assertEqual(
+                    fragments.generate_fragment_ion_annotations(ion_types=ion_types, order=order), annotations
+                )
+
+            order = ("ion_type", "position", "charge")
+            annotations = [
+                (ion_type, pos, charge) for ion_type in ion_types for pos in c.POSITIONS for charge in c.CHARGES
+            ]
+            with self.subTest(order=order, ion_types=ion_types):
+                self.assertEqual(
+                    fragments.generate_fragment_ion_annotations(ion_types=ion_types, order=order), annotations
+                )
+
+    def test_catches_redundant_order(self):
+        """Check if redundant order is caught."""
+        with self.assertRaises(ValueError):
+            _ = fragments.generate_fragment_ion_annotations(
+                ion_types=["y", "b"], order=("ion_type", "position", "ion_type")
+            )
+
+
+class TestNeutralLossFunctions(unittest.TestCase):
+    """Tests for neutral loss annotation."""
+
+    def test_add_nl(self):
+        """Test the _add_nl function with a range of amino acids and neutral losses."""
+        neutral_losses = ["H2O", "NH3"]
+        nl_dict = {
+            0: ["CO2"],  # Initial dictionary contains CO2 for index 0
+            1: ["H2O"],  # Initial dictionary contains H2O for index 1
+        }
+        start_aa_index = 0
+        end_aa_index = 2  # Only indices 0 and 1 will be modified
+
+        # Expected output after the neutral losses are added
+        expected_nl_dict = {
+            0: ["CO2", "H2O", "NH3"],  # Both H2O and NH3 added
+            1: ["H2O", "NH3"],  # NH3 added, H2O already present
+        }
+
+        result = fragments._add_nl(neutral_losses, nl_dict, start_aa_index, end_aa_index)
+        self.assertEqual(result, expected_nl_dict)
+
+    def test_calculate_nl_score_mass(self):
+        """Test the _calculate_nl_score_mass function with various neutral losses."""
+        # Test for H2O, which should reduce the score by 5
+        score, mass = fragments._calculate_nl_score_mass("H2O")
+        self.assertEqual(score, 95)  # Starting score of 100 - 5
+        self.assertEqual(mass, 18.01056467)  # Mass of H2O
+
+        # Test for NH3, which should also reduce the score by 5
+        score, mass = fragments._calculate_nl_score_mass("NH3")
+        self.assertEqual(score, 95)  # Starting score of 100 - 5
+        self.assertEqual(mass, 17.026549105)  # Mass of NH3
+
+        # Test for CO2, which should reduce the score by 30
+        score, mass = fragments._calculate_nl_score_mass("CO2")
+        self.assertEqual(score, 70)  # Starting score of 100 - 30
+        self.assertEqual(mass, 43.9898292)  # Mass of CO2
+
+        # Test for C2H4O2, which should reduce the score by 30
+        score, mass = fragments._calculate_nl_score_mass("C2H4O2")
+        self.assertEqual(score, 70)  # Starting score of 100 - 30
+        self.assertEqual(mass, 60.02112934)
diff --git a/tests/unit_tests/test_mod_string.py b/tests/unit_tests/test_mod_string.py
index 6edc124..6d5d78d 100644
--- a/tests/unit_tests/test_mod_string.py
+++ b/tests/unit_tests/test_mod_string.py
@@ -1,7 +1,7 @@
 import unittest
 
+import spectrum_fundamentals.constants as c
 import spectrum_fundamentals.mod_string as mod
-from spectrum_fundamentals.constants import ALPHABET
 
 
 class TestMSP:
@@ -19,23 +19,43 @@ def test_internal_to_mod_names(self):
 
 
 class TestSageToInternal(unittest.TestCase):
-    """Class to test MaxQuant to internal."""
+    """Class to test Sage to internal."""
 
     def test_sage_to_internal_carbamidomethylation(self):
-        """Test maxquant_to_internal_carbamidomethylation."""
-        self.assertEqual(mod.sage_to_internal(["ABC[+57.0214]DEFGH"]), ["ABC[UNIMOD:4]DEFGH"])
+        """Test sage_to_internal_carbamidomethylation."""
+        self.assertEqual(mod.sage_to_internal(["ABC[+57.0215]DEFGH"], c.MOD_MASSES_SAGE), ["ABC[UNIMOD:4]DEFGH"])
 
     def test_sage_to_internal_variable_oxidation(self):
-        """Test maxquant_to_internal_variable_oxidation."""
-        self.assertEqual(mod.sage_to_internal(["ABC[+57.0214]DM[+15.9949]EFGH"]), ["ABC[UNIMOD:4]DM[UNIMOD:35]EFGH"])
+        """Test sage_to_internal_variable_oxidation."""
+        self.assertEqual(
+            mod.sage_to_internal(["ABC[+57.0215]DM[+15.9949]EFGH"], c.MOD_MASSES_SAGE),
+            ["ABC[UNIMOD:4]DM[UNIMOD:35]EFGH"],
+        )
 
     def test_sage_to_internal_tmt(self):
-        """Test maxquant_to_internal_tmt."""
+        """Test sage_to_internal_tmt."""
         self.assertEqual(
-            mod.sage_to_internal(["[+229.1629]-ABC[+57.0214]DEFGHK[+229.1629]"]),
+            mod.sage_to_internal(["[+229.1629]-ABC[+57.0215]DEFGHK[+229.1629]"], c.MOD_MASSES_SAGE),
             ["[UNIMOD:737]-ABC[UNIMOD:4]DEFGHK[UNIMOD:737]"],
         )
 
+    def test_sage_to_internal_custom(self):
+        """Test sage_to_internal_custom."""
+        # difference in rounding
+        mods = {**c.MOD_MASSES_SAGE, **{"229.1628": "[UNIMOD:737]"}}
+        self.assertEqual(
+            mod.sage_to_internal(["[+229.1628]-ABC[+57.0215]DEFGHK[+229.1629]"], mods),
+            ["[UNIMOD:737]-ABC[UNIMOD:4]DEFGHK[UNIMOD:737]"],
+        )
+
+    def test_sage_to_internal_custom_overwrite(self):
+        """Test sage_to_internal_custom_overwrite."""
+        mods = {**c.MOD_MASSES_SAGE, **{"57.0215": "[UNIMOD:977]"}}
+        self.assertEqual(
+            mod.sage_to_internal(["[+229.1629]-ABC[+57.0215]DEFGHK[+229.1629]"], mods),
+            ["[UNIMOD:737]-ABC[UNIMOD:977]DEFGHK[UNIMOD:737]"],
+        )
+
 
 class TestXisearchToInternal(unittest.TestCase):
     """Class to test Internal to Xisearch."""
@@ -89,53 +109,99 @@ class TestMaxQuantToInternal(unittest.TestCase):
 
     def test_maxquant_to_internal_carbamidomethylation(self):
         """Test maxquant_to_internal_carbamidomethylation."""
-        self.assertEqual(mod.maxquant_to_internal(["_ABCDEFGH_"]), ["ABC[UNIMOD:4]DEFGH"])
+        mods = {**c.MAXQUANT_VAR_MODS, **{"C": "C[UNIMOD:4]"}}
+        self.assertEqual(mod.maxquant_to_internal(["_ABCDEFGH_"], mods=mods), ["ABC[UNIMOD:4]DEFGH"])
 
     def test_maxquant_to_internal_variable_oxidation(self):
         """Test maxquant_to_internal_variable_oxidation."""
-        self.assertEqual(mod.maxquant_to_internal(["_ABCDM(ox)EFGH_"]), ["ABC[UNIMOD:4]DM[UNIMOD:35]EFGH"])
+        mods = {**c.MAXQUANT_VAR_MODS, **{"C": "C[UNIMOD:4]"}}
+        self.assertEqual(mod.maxquant_to_internal(["_ABCDM(ox)EFGH_"], mods=mods), ["ABC[UNIMOD:4]DM[UNIMOD:35]EFGH"])
 
     def test_maxquant_to_internal_variable_oxidation_long(self):
         """Test maxquant_to_internal_variable_oxidation_long."""
-        self.assertEqual(mod.maxquant_to_internal(["_ABCDM(Oxidation (M))EFGH_"]), ["ABC[UNIMOD:4]DM[UNIMOD:35]EFGH"])
+        mods = {**c.MAXQUANT_VAR_MODS, **{"C": "C[UNIMOD:4]"}}
+        self.assertEqual(
+            mod.maxquant_to_internal(["_ABCDM(Oxidation (M))EFGH_"], mods=mods), ["ABC[UNIMOD:4]DM[UNIMOD:35]EFGH"]
+        )
 
     def test_maxquant_to_internal_variable_dehydration_long(self):
         """Test maxquant_to_internal_variable_dehydration_long."""
-        self.assertEqual(mod.maxquant_to_internal(["_ABCDS(Dehydrated (ST))EFGH_"]), ["ABC[UNIMOD:4]DS[UNIMOD:23]EFGH"])
+        mods = {**c.MAXQUANT_VAR_MODS, **{"C": "C[UNIMOD:4]"}}
+        self.assertEqual(
+            mod.maxquant_to_internal(["_ABCDS(Dehydrated (ST))EFGH_"], mods=mods), ["ABC[UNIMOD:4]DS[UNIMOD:23]EFGH"]
+        )
 
     def test_maxquant_to_internal_tmt(self):
         """Test maxquant_to_internal_tmt."""
         fixed_mods = {"C": "C[UNIMOD:4]", "^_": "_[UNIMOD:737]-", "K": "K[UNIMOD:737]"}
+        mods = {**c.MAXQUANT_VAR_MODS, **fixed_mods}
         self.assertEqual(
-            mod.maxquant_to_internal(["_ABCDEFGHK_"], fixed_mods), ["[UNIMOD:737]-ABC[UNIMOD:4]DEFGHK[UNIMOD:737]"]
+            mod.maxquant_to_internal(["_ABCDEFGHK_"], mods=mods), ["[UNIMOD:737]-ABC[UNIMOD:4]DEFGHK[UNIMOD:737]"]
         )
 
-    def test_maxquant_to_internal_silac(self):
-        """Test maxquant_to_internal_silac."""
-        fixed_mods = {"C": "C[UNIMOD:4]", "K": "K[UNIMOD:259]", "R": "R[UNIMOD:267]"}
+    def test_maxquant_to_internal_custom_stat_overwrite(self):
+        # overwrite fixed_mod with stat mod
+        """Test maxquant_to_internal_custom_stat_overwrite."""
+        fixed_mods = {"C": "C[UNIMOD:4]", "^_": "_[UNIMOD:737]-", "K": "K[UNIMOD:737]"}
+        stat_mod = {"K": "[UNIMOD:738]"}
+        mods = {**c.MAXQUANT_VAR_MODS, **fixed_mods, **stat_mod}
         self.assertEqual(
-            mod.maxquant_to_internal(["_ABCDEFGHRK_"], fixed_mods), ["ABC[UNIMOD:4]DEFGHR[UNIMOD:267]K[UNIMOD:259]"]
+            mod.maxquant_to_internal(["_ABCDEFGHK_"], mods=mods), ["[UNIMOD:737]-ABC[UNIMOD:4]DEFGHK[UNIMOD:738]"]
         )
 
+    def test_maxquant_to_internal_custom_var(self):
+        # overwrite maxquant_var_mod
+        """Test maxquant_to_internal_custom_var."""
+        fixed_mods = {"C": "C[UNIMOD:4]"}
+        var_mod = {"(ox)": "[UNIMOD:425]"}
+        mods = {**c.MAXQUANT_VAR_MODS, **fixed_mods, **var_mod}
+        self.assertEqual(mod.maxquant_to_internal(["_ABCDM(ox)EFGH_"], mods=mods), ["ABC[UNIMOD:4]DM[UNIMOD:425]EFGH"])
+
+    def test_maxquant_to_internal_custom_stat(self):
+        # overwrite maxquant_var_mod
+        """Test maxquant_to_internal_custom_var."""
+        fixed_mods = {"C": "C[UNIMOD:4]"}
+        stat_mod = {"M": "[UNIMOD:425]"}
+        mods = {**c.MAXQUANT_VAR_MODS, **fixed_mods, **stat_mod}
+        self.assertEqual(mod.maxquant_to_internal(["_ABCDMEFGH_"], mods=mods), ["ABC[UNIMOD:4]DM[UNIMOD:425]EFGH"])
+
 
 class TestMSFraggerToInternal(unittest.TestCase):
     """Class to test MSFragger to internal."""
 
     def test_msfragger_to_internal_carbamidomethylation(self):
         """Test msfragger_to_internal_carbamidomethylation."""
-        self.assertEqual(mod.msfragger_to_internal(["ABCDEFGH"]), ["ABC[UNIMOD:4]DEFGH"])
+        mods = {**c.MSFRAGGER_VAR_MODS, **{"C": "C[UNIMOD:4]"}}
+        self.assertEqual(mod.msfragger_to_internal(["ABCDEFGH"], mods), ["ABC[UNIMOD:4]DEFGH"])
 
     def test_msfragger_to_internal_variable_oxidation(self):
         """Test msfragger_to_internal_variable_oxidation."""
-        self.assertEqual(mod.msfragger_to_internal(["ABCDM[147]EFGH"]), ["ABC[UNIMOD:4]DM[UNIMOD:35]EFGH"])
+        mods = {**c.MSFRAGGER_VAR_MODS, **{"C": "C[UNIMOD:4]"}}
+        self.assertEqual(mod.msfragger_to_internal(["ABCDM[147]EFGH"], mods), ["ABC[UNIMOD:4]DM[UNIMOD:35]EFGH"])
 
     def test_msfragger_to_internal_tmt(self):
         """Test msfragger_to_internal_tmt."""
         fixed_mods = {"C": "C[UNIMOD:4]", r"n[\d+]": "[UNIMOD:737]-", "K": "K[UNIMOD:737]"}
         self.assertEqual(
-            mod.msfragger_to_internal(["n[230]ABCDEFGHK"], fixed_mods), ["[UNIMOD:737]-ABC[UNIMOD:4]DEFGHK[UNIMOD:737]"]
+            mod.msfragger_to_internal(["n[230]ABCDEFGHK"], {**c.MSFRAGGER_VAR_MODS, **fixed_mods}),
+            ["[UNIMOD:737]-ABC[UNIMOD:4]DEFGHK[UNIMOD:737]"],
         )
 
+    def test_msfragger_to_internal_ms_custom_mod(self):
+        """Test msfragger_to_internal_ms_custom_mod."""
+        fixed_mods = {"C": "C[UNIMOD:4]"}
+        custom_mod = {"M[35]": "[UNIMOD:35]"}
+        mods = {**c.MSFRAGGER_VAR_MODS, **fixed_mods, **custom_mod}
+        self.assertEqual(
+            mod.msfragger_to_internal(["n[230]ABCDEFGHM[35]"], mods), ["[UNIMOD:737]-ABC[UNIMOD:4]DEFGHM[UNIMOD:35]"]
+        )
+
+    def test_msfragger_to_internal_custom_mod(self):
+        """Test msfragger_to_internal_custom_mod."""
+        custom_mod = {"M[35]": "[UNIMOD:35]", "(cm)": "[UNIMOD:4]"}
+        mods = {**c.MSFRAGGER_VAR_MODS, **custom_mod}
+        self.assertEqual(mod.msfragger_to_internal(["ABC(cm)DEFGHM[35]"], mods), ["ABC[UNIMOD:4]DEFGHM[UNIMOD:35]"])
+
 
 class TestInternalToSpectronaut(unittest.TestCase):
     """Class to test Internal to Spectronaut."""
@@ -160,7 +226,7 @@ def test_internal_to_spectronaut_variable_dehydration_long(self):
 
 
 class TestInternalTransformations(unittest.TestCase):
-    """Class to test internal to interla without mods."""
+    """Class to test internal to interal without mods."""
 
     def test_internal_without_mods(self):
         """Test internal with mods to internal without_mods."""
@@ -173,6 +239,14 @@ def test_internal_to_mod_masses(self):
             ["[+229.162932]-ABC[+57.021464]DEFGHK[+229.162932]"],
         )
 
+    def test_internal_to_mod_masses_custom(self):
+        """Test internal with custom mods to internal without_mods."""
+        mods = {"[UNIMOD:977]": 57.0215}
+        self.assertEqual(
+            mod.internal_to_mod_mass(["[UNIMOD:737]-ABC[UNIMOD:977]DEFGHK[UNIMOD:737]"], mods),
+            ["[+229.162932]-ABC[+57.0215]DEFGHK[+229.162932]"],
+        )
+
     def test_proteomicsdb_to_internal(self):
         """Test proteomicsdb sequence to internal sequence with fixed and variable modifications."""
         prdb_sequence = "AAMCGHK"
@@ -215,22 +289,102 @@ def test_parse_modstrings(self):
         """Test parse_modstrings with only valid elements."""
         valid_seq = ["A", "C[UNIMOD:4]", "C[UNIMOD:4]", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N"]
         valid_seq.extend(["M[UNIMOD:35]", "P", "Q", "R", "S", "T", "V", "W", "Y", "M[UNIMOD:35]", "S", "T", "Y"])
-        self.assertEqual(next(mod.parse_modstrings(["".join(valid_seq)], alphabet=ALPHABET)), valid_seq)
+        self.assertEqual(next(mod.parse_modstrings(["".join(valid_seq)], alphabet=c.ALPHABET)), valid_seq)
 
     def test_parse_modstrings_with_translation(self):
         """Test parse_modstrings with only valid elements."""
         valid_seq = ["A", "C[UNIMOD:4]", "C[UNIMOD:4]", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N"]
         valid_seq.extend(["M[UNIMOD:35]", "P", "Q", "R", "S", "T", "V", "W", "Y", "M[UNIMOD:35]", "S", "T", "Y"])
-        values = [ALPHABET[elem] for elem in valid_seq]
-        self.assertEqual(next(mod.parse_modstrings(["".join(valid_seq)], alphabet=ALPHABET, translate=True)), values)
+        values = [c.ALPHABET[elem] for elem in valid_seq]
+        self.assertEqual(next(mod.parse_modstrings(["".join(valid_seq)], alphabet=c.ALPHABET, translate=True)), values)
 
     def test_parse_modstrings_invalid(self):
         """Test correct behaviour of  parse_modstrings when invalid sequence is encountered."""
         invalid_seq = "SEQUENCE"
-        generator_yielding_invalid = mod.parse_modstrings([invalid_seq], alphabet=ALPHABET)
+        generator_yielding_invalid = mod.parse_modstrings([invalid_seq], alphabet=c.ALPHABET)
         self.assertRaises(ValueError, list, generator_yielding_invalid)
 
     def test_parse_modstrings_invalid_with_filtering(self):
         """Test correct behaviour of parse_modstrings when invalid sequence is handled."""
         invalid_seq = "testing"
-        self.assertEqual(next(mod.parse_modstrings([invalid_seq], alphabet=ALPHABET, filter=True)), [0])
+        self.assertEqual(next(mod.parse_modstrings([invalid_seq], alphabet=c.ALPHABET, filter=True)), [0])
+
+    def test_get_all_tokens(self):
+        """Test parsing of any UNIMOD sequence into tokens."""
+        seqs = ["ACKC[UNIMOD:4]AD", "PEPTIDE", "PEM[UNIMOD:35]"]
+
+        result = mod.get_all_tokens(seqs)
+        self.assertEqual(result, {"A", "C", "C[UNIMOD:4]", "D", "E", "I", "K", "M[UNIMOD:35]", "P", "T"})
+
+
+class TestCustomToInternal(unittest.TestCase):
+    """Class to test custom to internal."""
+
+    def test_custom_to_internal_carbamidomethylation(self):
+        """Test custom_to_internal_carbamidomethylation."""
+        mods = {"C": "C[UNIMOD:4]"}
+        self.assertEqual(mod.custom_to_internal(["ABCDEFGH"], mods), ["ABC[UNIMOD:4]DEFGH"])
+
+    def test_custom_to_internal_custom_mods(self):
+        """Test custom_to_internal_custom_mods."""
+        fixed_mods = {"C": "C[UNIMOD:4]"}
+        custom_mod = {"M[35]": "[UNIMOD:35]"}
+        mods = {**fixed_mods, **custom_mod}
+        self.assertEqual(mod.custom_to_internal(["ABCDEFGHM[35]"], mods), ["ABC[UNIMOD:4]DEFGHM[UNIMOD:35]"])
+
+
+class TestAddPermutations(unittest.TestCase):
+    """Class to test add permutations."""
+
+    def test_no_modifications(self):
+        """Test case where no modifications are present in the sequence."""
+        modified_sequence = "PEPTIDE"
+        unimod_id = 123
+        residues = ["P", "E"]
+        result = mod.add_permutations(modified_sequence, unimod_id, residues)
+        self.assertEqual(result, ["PEPTIDE"])
+
+    def test_single_modification(self):
+        """Test case with a single modification."""
+        modified_sequence = "P[UNIMOD:123]EPTIDE"
+        unimod_id = 123
+        residues = ["P", "E"]
+        result = mod.add_permutations(modified_sequence, unimod_id, residues)
+        expected_result = ["PEPTIDE[UNIMOD:123]", "PEP[UNIMOD:123]TIDE", "PE[UNIMOD:123]PTIDE", "P[UNIMOD:123]EPTIDE"]
+        self.assertEqual(result, expected_result)
+
+    def test_multiple_modifications(self):
+        """Test case with multiple modifications."""
+        modified_sequence = "PEP[UNIMOD:123]TIDE[UNIMOD:123]"
+        unimod_id = 123
+        residues = ["P", "E"]
+        result = mod.add_permutations(modified_sequence, unimod_id, residues)
+        expected_result = [
+            "PEP[UNIMOD:123]TIDE[UNIMOD:123]",
+            "PE[UNIMOD:123]PTIDE[UNIMOD:123]",
+            "P[UNIMOD:123]EPTIDE[UNIMOD:123]",
+            "PE[UNIMOD:123]P[UNIMOD:123]TIDE",
+            "P[UNIMOD:123]EP[UNIMOD:123]TIDE",
+            "P[UNIMOD:123]E[UNIMOD:123]PTIDE",
+        ]
+        self.assertEqual(result, expected_result)
+
+    def test_check_monoisotopic_peak_enabled(self):
+        """Test case with check_monoisotopic_peak flag enabled."""
+        modified_sequence = "PEP[UNIMOD:123]TID[UNIMOD:123]E"
+        unimod_id = 123
+        residues = ["P", "E"]
+        result = mod.add_permutations(modified_sequence, unimod_id, residues, allow_one_less_modification=True)
+        expected_result = [
+            "PEP[UNIMOD:123]TIDE[UNIMOD:123]",
+            "PE[UNIMOD:123]PTIDE[UNIMOD:123]",
+            "P[UNIMOD:123]EPTIDE[UNIMOD:123]",
+            "PE[UNIMOD:123]P[UNIMOD:123]TIDE",
+            "P[UNIMOD:123]EP[UNIMOD:123]TIDE",
+            "P[UNIMOD:123]E[UNIMOD:123]PTIDE",
+            "PEPTIDE[UNIMOD:123]",
+            "PEP[UNIMOD:123]TIDE",
+            "PE[UNIMOD:123]PTIDE",
+            "P[UNIMOD:123]EPTIDE",
+        ]
+        self.assertEqual(result, expected_result)
diff --git a/tests/unit_tests/test_percolator.py b/tests/unit_tests/test_percolator.py
index 6a2de87..3651d21 100644
--- a/tests/unit_tests/test_percolator.py
+++ b/tests/unit_tests/test_percolator.py
@@ -186,7 +186,7 @@ def test_linear_not_sorted(self):
 
     def test_noisy_logistic(self):
         """Test get_aligned_predicted_retention_times for a more realistic, similar to logistic case."""
-        methods = ["lowess", "spline", "logistic"]
+        methods = ["spline", "logistic"]
         x, y, correct_y = _create_noisy_logistic_data()
         for method in methods:
             self._get_aligned_predicted_retention_times_noisy_logistic_error(x, y, correct_y, method)
@@ -315,6 +315,41 @@ def test_get_delta_score(self):
             perc.Percolator.get_delta_score(df, "spectral_angle"), np.array([20, 40, 0, 40, 250, 0])
         )
 
+    def test_add_additional_features(self):
+        """Test add_additional_features."""
+        types = {
+            "RAW_FILE": str,
+            "SCAN_NUMBER": int,
+            "MODIFIED_SEQUENCE": str,
+            "PRECURSOR_CHARGE": int,
+            "SCAN_EVENT_NUMBER": int,
+            "MASS": float,
+            "SCORE": float,
+            "REVERSE": int,
+            "SEQUENCE": str,
+            "PEPTIDE_LENGTH": float,
+            "A": float,
+            "B": float,
+            "precursor_charge": float,
+            "Unnamed 1": int,
+        }
+
+        perc_input = pd.DataFrame(columns=types).astype(types)
+
+        percolator_all = perc.Percolator(metadata=perc_input, input_type="rescore", additional_columns="all")
+        percolator_all.add_additional_features()
+        pd.testing.assert_frame_equal(
+            pd.DataFrame(columns=["A", "B"]).astype({"A": float, "B": float}), percolator_all.metrics_val
+        )
+
+        percolator_list = perc.Percolator(metadata=perc_input, input_type="rescore", additional_columns=["A"])
+        percolator_list.add_additional_features()
+        pd.testing.assert_frame_equal(pd.DataFrame(columns=["A"]).astype({"A": float}), percolator_list.metrics_val)
+
+        percolator_none = perc.Percolator(metadata=perc_input, input_type="rescore", additional_columns="none")
+        percolator_none.add_additional_features()
+        pd.testing.assert_frame_equal(pd.DataFrame(), percolator_none.metrics_val)
+
     def test_calc(self):
         """Test calc."""
         perc_input = pd.read_csv(Path(__file__).parent / "data/perc_input.csv")
@@ -360,7 +395,7 @@ def test_calc(self):
         # np.testing.assert_almost_equal(percolator.metrics_val['ExpMass'][0], 900.50345678)
         np.testing.assert_string_equal(percolator.metrics_val["Peptide"][0], "_.AAIGEATRL._")
         np.testing.assert_string_equal(
-            percolator.metrics_val["Proteins"][0], "AAIGEATRL"
+            percolator.metrics_val["Proteins"][0], "sp|O23523|RGGA_ARATH"
         )  # we don't need the protein ID to get PSM / peptide results
 
         # features