diff --git a/.github/workflows/legacy_create_release.yml b/.github/workflows/legacy_create_release.yml
deleted file mode 100644
index 161d9898..00000000
--- a/.github/workflows/legacy_create_release.yml
+++ /dev/null
@@ -1,201 +0,0 @@
-# TODO delete once the new release workflow has run once
-on:
-  workflow_dispatch:
-    inputs:
-      commit_to_release:
-        description: 'Enter commit hash to release (example: ef4037cb571f99cb4919b520fde7174972aae473)'
-        required: true
-      tag_to_release:
-        description: 'Enter tag to release (example: v1.5.5)'
-        required: true
-
-
-name: LEGACY Create Draft Release
-
-jobs:
-  Get_New_Version:
-    runs-on: ubuntu-latest
-    outputs:
-      new_version: ${{ steps.check_release_tag.outputs.new_version }}
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-        with:
-          ref: ${{ inputs.commit_to_release }}
-
-      - name: Check release tag
-        id: check_release_tag
-        shell: bash -le {0}
-        run: |
-          CURRENT_VERSION=$(./misc/get_current_version.sh)
-          if [ "v${CURRENT_VERSION}" != "${{ inputs.tag_to_release }}" ]; then
-            echo Code version "v${CURRENT_VERSION}" does not match the tag to release ${{ inputs.tag_to_release }}
-            exit 1
-          fi
-          echo "new_version=$CURRENT_VERSION" >> $GITHUB_OUTPUT
-
-      - uses: mukunku/tag-exists-action@v1.6.0
-        id: check-tag
-        with:
-          tag: ${{ inputs.tag_to_release }}
-
-      - name: Check if tag already exists
-        run: |
-          echo "Tag already exists!"
-          exit 1
-        if: steps.check-tag.outputs.exists == 'true'
-
-
-  Create_Draft_Release:
-    runs-on: ubuntu-latest
-    needs: Get_New_Version
-    outputs:
-      upload_url: ${{ steps.draft_release.outputs.upload_url }}
-    steps:
-      - name: Draft Release
-        id: draft_release
-        # TODO this action is deprecated, replace with https://github.com/ncipollo/release-action
-        # cf. https://github.com/actions/create-release/issues/119#issuecomment-783010321
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          tag_name: ${{ inputs.tag_to_release }}
-          release_name: ${{ inputs.tag_to_release }}
-          draft: true
-          prerelease: false
-
-  Create_MacOS_Installer:
-    needs: [Create_Draft_Release, Get_New_Version]
-    env:
-        ARCH: x64
-        EAGER_IMPORT: true
-    runs-on: macos-latest-xlarge
-    steps:
-    - name : Checkout code
-      uses: actions/checkout@v4
-      with:
-        ref: ${{ inputs.commit_to_release }}
-
-    # Build backend
-    - name: Install conda
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        miniconda-version: "latest"
-        auto-update-conda: true
-        activate-environment: alpha
-        python-version: "3.11"
-
-    - name: Check arm64
-      shell: bash -el {0}
-      run: |
-        python -c "import platform; print(platform.machine())"
-
-    - name: Build backend
-      shell: bash -el {0}
-      run: |
-        release/macos/build_backend_macos.sh
-
-    - name: Test backend
-      shell: bash -el {0}
-      run: |
-        dist/alphadia/alphadia --version
-
-    # Build GUI
-    - name: Setup Node.js
-      uses: actions/setup-node@v4
-
-    - name: Build GUI
-      run: |
-        release/macos/build_gui_macos.sh
-
-    # combine backend and GUI
-    - name: Build package
-      shell: bash -el {0}
-      run: |
-        release/macos/build_pkg_macos.sh
-
-    - name: List output files
-      run: |
-        ls dist
-
-    # Upload the package
-    - name: Upload a Release Asset
-      uses: actions/upload-release-asset@v1
-      env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      with:
-          upload_url: ${{ needs.Create_Draft_Release.outputs.upload_url }}
-          asset_path: dist/alphadia-${{ needs.Get_New_Version.outputs.new_version }}-darwin-${{ env.ARCH }}.pkg
-          asset_name: alphadia-${{ needs.Get_New_Version.outputs.new_version }}-darwin-${{ env.ARCH }}.pkg
-          asset_content_type: application/zip
-
-  Create_Windows_Installer:
-    needs: [Create_Draft_Release, Get_New_Version]
-    env:
-        ARCH: x64
-    runs-on: windows-latest
-    steps:
-    - name : Checkout code
-      uses: actions/checkout@v4
-      with:
-        ref: ${{ inputs.commit_to_release }}
-
-    # Build backend
-    - name: Install conda
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        miniconda-version: "latest"
-        auto-update-conda: true
-        activate-environment: alpha
-        python-version: "3.11"
-
-    - name: Build Backend
-      shell: powershell
-      run: |
-        release/windows/build_backend.ps1
-
-    - name: Test Backend
-      shell: powershell
-      run: |
-        dist\alphadia\alphadia.exe --version
-
-    # Build GUI
-    - name: Setup Node.js
-      uses: actions/setup-node@v4
-
-    - name: Build GUI
-      shell: powershell
-      run: |
-        release/windows/build_gui.ps1
-
-    # combine backend and GUI
-    - name: Check if Innosetup is installed
-      shell: powershell
-      run: |
-        if (-not (Test-Path "C:\Program Files (x86)\Inno Setup 6\ISCC.exe")) {
-          Write-Host "Inno Setup is not installed"
-          exit 1
-        }
-        else {
-          Write-Host "Inno Setup is installed"
-        }
-
-    - name: Build Installer
-      shell: powershell
-      run: |
-        release/windows/build_installer.ps1
-
-    - name: List output files
-      run: |
-        ls dist
-
-    - name: Upload a Release Asset
-      uses: actions/upload-release-asset@v1
-      env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      with:
-          upload_url: ${{ needs.Create_Draft_Release.outputs.upload_url }}
-          asset_path: dist/alphadia-${{ needs.Get_New_Version.outputs.new_version }}-win-${{ env.ARCH }}.exe
-          asset_name: alphadia-${{ needs.Get_New_Version.outputs.new_version }}-win-${{ env.ARCH }}.exe
-          asset_content_type: application/zip
diff --git a/.github/workflows/legacy_publish_on_pypi.yml b/.github/workflows/legacy_publish_on_pypi.yml
deleted file mode 100644
index 2efb2470..00000000
--- a/.github/workflows/legacy_publish_on_pypi.yml
+++ /dev/null
@@ -1,126 +0,0 @@
-# TODO delete once the new release workflow has run once
-on:
-  workflow_dispatch:
-    inputs:
-      tag_to_release:
-        description: 'Enter tag to release (example: v1.5.5)'
-        required: true
-
-name: LEGACY Publish on PyPi
-
-env:
-  PYTHON_VERSION: "3.11"
-
-jobs:
-  Create_PyPi_Release:
-    runs-on: ubuntu-latest
-    outputs:
-      new_version: ${{ steps.get_current_version.outputs.new_version }}
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          ref: ${{ inputs.tag_to_release }}
-      - uses: conda-incubator/setup-miniconda@v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          python-version: ${{ env.PYTHON_VERSION }}
-      - name: Conda info
-        shell: bash -le {0}
-        run: conda info
-      - name: Get current version
-        id: get_current_version
-        shell: bash -l {0}
-        run: |
-         CURRENT_VERSION=$(./misc/get_current_version.sh)
-         echo "new_version=$CURRENT_VERSION" >> $GITHUB_OUTPUT
-      - uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
-      - name: Prepare distribution
-        shell: bash -le {0}
-        run: |
-          conda create -n alphadia_build python=${{ env.PYTHON_VERSION }} -y
-          conda activate alphadia_build
-          python -m pip install --upgrade pip
-          pip install build twine
-          rm -rf dist
-          rm -rf build
-          python -m build
-          twine check dist/*
-          conda deactivate
-          conda env remove --name alphadia_build -y
-          conda clean --all -y
-      - name: Publish distribution to Test-PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          repository-url: https://test.pypi.org/legacy/
-          user: __token__
-          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-      - name: Test Test-PyPI loose installation
-        shell: bash -le {0}
-        run: |
-          conda create -n pip_loose_test python=${{ env.PYTHON_VERSION }} -y
-          conda activate pip_loose_test
-          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "alphadia==${{ steps.get_current_version.outputs.new_version }}"
-          alphadia -v
-          conda deactivate
-          conda env remove --name pip_stable_test -y
-          conda clean --all -y
-      - name: Test Test-PyPI stable installation
-        shell: bash -le {0}
-        run: |
-          conda create -n pip_stable_test python=${{ env.PYTHON_VERSION }} -y
-          conda activate pip_stable_test
-          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "alphadia[stable]==${{ steps.get_current_version.outputs.new_version }}"
-          alphadia -v
-          conda deactivate
-          conda env remove --name pip_stable_test -y
-          conda clean --all -y
-      - name: Publish distribution to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
-  Test_PyPi_Release:
-    name: Test_PyPi_version_on_${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    needs: Create_PyPi_Release
-    strategy:
-      matrix:
-        os: [ubuntu-latest, macOS-latest, windows-latest]
-    steps:
-      - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          python-version: ${{ env.PYTHON_VERSION }}
-      - name: Conda info
-        shell: bash -le {0}
-        run: conda info
-      - uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
-      - name: Test PyPI stable installation
-        shell: bash -le {0}
-        run: |
-          conda create -n pip_stable python=${{ env.PYTHON_VERSION }} -y
-          conda activate pip_stable
-          pip install "alphadia[stable]==${{ needs.Create_PyPi_Release.outputs.new_version }}"
-          alphadia -v
-          conda deactivate
-          conda env remove --name pip_stable -y
-          conda clean --all -y
-      - name: Test PyPI loose installation
-        shell: bash -le {0}
-        run: |
-          conda create -n pip_loose python=${{ env.PYTHON_VERSION }} -y
-          conda activate pip_loose
-          pip install alphadia==${{ needs.Create_PyPi_Release.outputs.new_version }}
-          alphadia -v
-          conda deactivate
-          conda env remove --name pip_loose -y
-          conda clean --all -y
diff --git a/misc/.bumpversion.cfg b/misc/.bumpversion.cfg
index f51e7b54..f9a7dadd 100644
--- a/misc/.bumpversion.cfg
+++ b/misc/.bumpversion.cfg
@@ -29,18 +29,11 @@ serialize =
 
 [bumpversion:file:../release/macos/build_package_macos.sh]
 
-[bumpversion:file:../release/macos/build_backend_macos.sh]
-
-[bumpversion:file:../release/macos/build_pkg_macos.sh]
-
 [bumpversion:file:../release/macos/distribution.xml]
 
 [bumpversion:file:../release/windows/alphadia_innoinstaller.iss]
 
-[bumpversion:file:../release/windows/alphadia_innoinstaller_old.iss]
-
 [bumpversion:file:../release/windows/build_installer_windows.ps1]
 
-[bumpversion:file:../release/windows/build_backend.ps1]
 search = {current_version}
 replace = {new_version}
diff --git a/release/macos/build_backend_macos.sh b/release/macos/build_backend_macos.sh
deleted file mode 100755
index ea713320..00000000
--- a/release/macos/build_backend_macos.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-# TODO remove with old release workflow
-
-# navigate to the root directory
-
-python -m build
-pip install "dist/alphadia-1.8.0-py3-none-any.whl[stable]"
-
-# Creating the stand-alone pyinstaller folder
-pip install pyinstaller
-pyinstaller release/pyinstaller/alphadia.spec -y
diff --git a/release/macos/build_pkg_macos.sh b/release/macos/build_pkg_macos.sh
deleted file mode 100755
index 1f2a7bd6..00000000
--- a/release/macos/build_pkg_macos.sh
+++ /dev/null
@@ -1,78 +0,0 @@
-#!/bin/bash
-# TODO remove with old release workflow
-
-# Set up package name and version
-PACKAGE_NAME="alphadia"
-PACKAGE_VERSION="1.8.0"
-
-ARCH=$(uname -m)
-if [ "$ARCH" == "x86_64" ]; then
-  ARCH="x64"
-fi
-echo "ARCH=${ARCH}" >> $GITHUB_ENV
-
-KERNEL=$(uname -s | tr '[:upper:]' '[:lower:]')
-
-BUILD_NAME="${PACKAGE_NAME}-${PACKAGE_VERSION}-${KERNEL}-${ARCH}"
-
-PKG_FOLDER="dist/alphadia.app"
-
-# Cleanup the package folder
-echo "Cleaning up the package folder"
-
-rm -rf $PKG_FOLDER
-
-# === Prepare structure ===
-echo "Preparing package structure"
-
-mkdir -p $PKG_FOLDER
-mkdir -p $PKG_FOLDER/Contents/Resources
-mkdir -p $PKG_FOLDER/Contents/MacOS
-mkdir -p $PKG_FOLDER/Contents/Frameworks
-
-
-
-# === Backend ===
-echo "Copying backend"
-
-BACKEND_BUILD="dist/alphadia"
-
-# Check if the backend build exists, otherwise exit with an error
-if [ ! -d "$BACKEND_BUILD" ]; then
-  echo "Backend build not found at $BACKEND_BUILD"
-  exit 1
-fi
-
-# Copy the backend
-cp -a ${BACKEND_BUILD}/. $PKG_FOLDER/Contents/Frameworks/
-
-
-# === GUI ===
-echo "Copying GUI"
-
-ls ./gui/out
-
-# Set the path to the GUI build
-GUI_BUILD="./gui/out/alphadia-gui-${KERNEL}-${ARCH}"
-
-# Check if the GUI build exists, otherwise exit with an error
-if [ ! -d "$GUI_BUILD" ]; then
-  echo "GUI build not found at $GUI_BUILD"
-  exit 1
-fi
-
-# Copy the electron forge build
-cp -a ${GUI_BUILD}/. $PKG_FOLDER/Contents/Frameworks/
-
-# === Resources ===
-echo "Copying resources"
-cp release/logos/alphadia.icns $PKG_FOLDER/Contents/Resources/
-cp release/logos/alphadia.png $PKG_FOLDER/Contents/Resources/
-cp release/macos/alphadia $PKG_FOLDER/Contents/MacOS/
-
-cp release/macos/Info.plist $PKG_FOLDER/Contents/
-
-#change permissions for entry script
-chmod +x $PKG_FOLDER/Contents/MacOS/alphadia
-
-pkgbuild --root $PKG_FOLDER --identifier de.mpg.biochem.alphadia.app --version $PACKAGE_VERSION --install-location /Applications/alphadia.app --scripts release/macos/scripts dist/$BUILD_NAME.pkg --nopayload
diff --git a/release/windows/alphadia_innoinstaller_old.iss b/release/windows/alphadia_innoinstaller_old.iss
deleted file mode 100644
index 58f0ef86..00000000
--- a/release/windows/alphadia_innoinstaller_old.iss
+++ /dev/null
@@ -1,54 +0,0 @@
-; Script generated by the Inno Setup Script Wizard.
-; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
-; # TODO remove with old release workflow
-
-#define MyAppName "AlphaDIA"
-#define MyAppVersion "1.8.0"
-#define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs"
-#define MyAppURL "https://github.com/MannLabs/alphadia"
-#define MyAppExeName "alphadia-gui.exe"
-
-[Setup]
-; NOTE: The value of AppId uniquely identifies this application. Do not use the same AppId value in installers for other applications.
-; (To generate a new GUID, click Tools | Generate GUID inside the IDE.)
-AppId={{alphadia_Mann_Labs_MPI}
-AppName={#MyAppName}
-AppVersion={#MyAppVersion}
-;AppVerName={#MyAppName} {#MyAppVersion}
-AppPublisher={#MyAppPublisher}
-AppPublisherURL={#MyAppURL}
-AppSupportURL={#MyAppURL}
-AppUpdatesURL={#MyAppURL}
-DefaultDirName={autopf}\{#MyAppName}
-DisableProgramGroupPage=yes
-LicenseFile=..\..\LICENSE.txt
-; Uncomment the following line to run in non administrative install mode (install for current user only.)
-PrivilegesRequired=lowest
-PrivilegesRequiredOverridesAllowed=dialog
-OutputDir=..\..\dist
-; example for BUILD_NAME: alphadia-1.9.0-win-x64
-OutputBaseFilename={#GetEnv('BUILD_NAME')}
-SetupIconFile=..\logos\alphadia.ico
-Compression=lzma
-SolidCompression=yes
-WizardStyle=modern
-
-[Languages]
-Name: "english"; MessagesFile: "compiler:Default.isl"
-
-[Tasks]
-Name: "desktopicon"; Description: "{cm:CreateDesktopIcon}"; GroupDescription: "{cm:AdditionalIcons}"; Flags: unchecked
-
-[Files]
-Source: "..\..\gui\out\alphadia-gui-win32-x64\{#MyAppExeName}"; DestDir: "{app}"; Flags: ignoreversion
-Source: "..\..\gui\out\alphadia-gui-win32-x64\*"; DestDir: "{app}"; Flags: ignoreversion recursesubdirs createallsubdirs
-Source: "..\..\dist\alphadia\*"; DestDir: "{app}"; Flags: ignoreversion recursesubdirs createallsubdirs
-
-; NOTE: Don't use "Flags: ignoreversion" on any shared system files
-
-[Icons]
-Name: "{autoprograms}\{#MyAppName}"; Filename: "{app}\{#MyAppExeName}"
-Name: "{autodesktop}\{#MyAppName}"; Filename: "{app}\{#MyAppExeName}"; Tasks: desktopicon
-
-[Run]
-Filename: "{app}\{#MyAppExeName}"; Description: "{cm:LaunchProgram,{#StringChange(MyAppName, '&', '&&')}}"; Flags: nowait postinstall skipifsilent
diff --git a/release/windows/build_backend.ps1 b/release/windows/build_backend.ps1
deleted file mode 100644
index 82543623..00000000
--- a/release/windows/build_backend.ps1
+++ /dev/null
@@ -1,12 +0,0 @@
-# TODO remove with old release workflow
-
-Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./build
-Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./dist
-
-pip install build
-python -m build
-pip install "dist/alphadia-1.8.0-py3-none-any.whl[stable]"
-
-# Creating the stand-alone pyinstaller folder
-pip install pyinstaller tbb
-pyinstaller release/pyinstaller/alphadia.spec -y
diff --git a/release/windows/build_gui.ps1 b/release/windows/build_gui.ps1
deleted file mode 100644
index 8503d72f..00000000
--- a/release/windows/build_gui.ps1
+++ /dev/null
@@ -1,14 +0,0 @@
-# TODO remove with old release workflow
-
-# Powershell script to build the GUI for Windows
-
-cd gui
-# delete old build using powershell
-Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./out
-Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./dist
-
-
-npm install
-npm run make
-
-cd ..
diff --git a/release/windows/build_installer.ps1 b/release/windows/build_installer.ps1
deleted file mode 100644
index feb8e965..00000000
--- a/release/windows/build_installer.ps1
+++ /dev/null
@@ -1,4 +0,0 @@
-# TODO remove with old release workflow
-
-
-&  "C:\Program Files (x86)\Inno Setup 6\ISCC.exe" .\release\windows\alphadia_innoinstaller_old.iss