diff --git a/tools/matchms/matchms_export_skyline_transition_list.ipynb b/tools/matchms/matchms_export_skyline_transition_list.ipynb
deleted file mode 100644
index cc875009..00000000
--- a/tools/matchms/matchms_export_skyline_transition_list.ipynb
+++ /dev/null
@@ -1,112 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from matchms.importing import load_from_msp\n",
-    "from matchms.exporting.metadata_export import get_metadata_as_array\n",
-    "\n",
-    "import pandas as pd"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "spectra_file = \"test-data/filtering/reduce_to_top_n_peaks.msp\"\n",
-    "name_key = 'compound_name'\n",
-    "cols_to_include = [name_key, 'retention_index', 'mz', 'intensity']"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 40,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "2024-11-06 14:26:01,189:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.\n",
-      "2024-11-06 14:26:01,190:WARNING:matchms:add_retention:None can't be converted to float.\n",
-      "2024-11-06 14:26:01,191:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.\n",
-      "2024-11-06 14:26:01,192:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.\n",
-      "2024-11-06 14:26:01,193:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.\n",
-      "2024-11-06 14:26:01,194:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.\n"
-     ]
-    }
-   ],
-   "source": [
-    "spectra = list(load_from_msp(spectra_file))\n",
-    "spectra_dict = {}\n",
-    "for spectrum in spectra:\n",
-    "    spectra_dict[spectrum.get(name_key)] = spectrum"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 41,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "spectra_metadata, cols = get_metadata_as_array(spectra)\n",
-    "spectra_metadata_df = pd.DataFrame(spectra_metadata)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 42,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "spectra_metadata_df['peaks'] = spectra_metadata_df[name_key].transform(lambda x: spectra_dict[x].peaks)\n",
-    "spectra_metadata_df['mz'] = spectra_metadata_df['peaks'].transform(lambda x: x.mz)\n",
-    "spectra_metadata_df['intensity'] = spectra_metadata_df['peaks'].transform(lambda x: x.intensities)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 43,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "spectra_metadata_df = spectra_metadata_df.explode(['mz', 'intensity']).reset_index(drop=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 45,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "result = spectra_metadata_df[cols_to_include].rename(columns={'compound_name': 'precursor name', 'retention_index': 'retention index'})"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "matchms",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.7"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}