diff --git a/tests/quicktests/run_pipeline_w_different_input_formats.ipynb b/tests/quicktests/run_pipeline_w_different_input_formats.ipynb
index 61617ef..564395a 100644
--- a/tests/quicktests/run_pipeline_w_different_input_formats.ipynb
+++ b/tests/quicktests/run_pipeline_w_different_input_formats.ipynb
@@ -2,39 +2,29 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "../../test_data/system_tests/quicktests does not yet exist\n",
-      "quicktests.zip successfully downloaded to ../../test_data/system_tests/quicktests.zip\n",
-      "quicktests.zip successfully unzipped\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "'../../test_data/system_tests/quicktests'"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "import alphabase\n",
+    "import os\n",
     "import alphabase.test_data_downloader\n",
     "\n",
-    "alphabase.test_data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/VJm70w0p2P86tE1\", output_dir=\"../test_data/system_tests\").download()"
+    "# Use the current working directory as a starting point\n",
+    "current_dir = os.getcwd()\n",
+    "\n",
+    "# Navigate up two levels to reach the project root\n",
+    "project_root = os.path.abspath(os.path.join(current_dir, '..', '..'))\n",
+    "\n",
+    "output_dir = os.path.join(project_root, 'test_data', 'system_tests')\n",
+    "\n",
+    "\n",
+    "# Now use the absolute path in the DataShareDownloader call\n",
+    "alphabase.test_data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/VJm70w0p2P86tE1\", output_dir=output_dir).download()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -51,25 +41,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "2024-10-16 15:35:28,476 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
-      "2024-10-16 15:35:28,557 - directlfq.utils - INFO - using input type diann_precursor_ms1_and_ms2\n",
-      "2024-10-16 15:35:28,678 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
-      "2024-10-16 15:35:29,872 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
-      "2024-10-16 15:35:29,873 - directlfq.protein_intensity_estimation - INFO - 46 lfq-groups total\n",
-      "2024-10-16 15:35:29,889 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
-      "2024-10-16 15:35:30,778 - directlfq.lfq_manager - INFO - Could not add additional columns to protein table, printing without additional columns.\n",
-      "2024-10-16 15:35:30,779 - directlfq.lfq_manager - INFO - Writing results files.\n",
-      "2024-10-16 15:35:30,826 - directlfq.lfq_manager - INFO - Analysis finished!\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import directlfq.lfq_manager as lfq_manager\n",
     "diann_quicktest_file_parquet = f\"{quicktest_folder_diann}/shortened_input.parquet\"\n",
@@ -79,61 +53,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "2024-10-16 15:35:30,839 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
-      "2024-10-16 15:35:31,025 - directlfq.utils - INFO - using input type diann_precursors\n",
-      "2024-10-16 15:35:31,077 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
-      "2024-10-16 15:35:31,078 - directlfq.normalization - INFO - to few values for normalization without missing values. Including missing values\n",
-      "2024-10-16 15:35:31,082 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
-      "2024-10-16 15:35:31,082 - directlfq.protein_intensity_estimation - INFO - 46 lfq-groups total\n",
-      "2024-10-16 15:35:31,098 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
-      "2024-10-16 15:35:31,623 - directlfq.lfq_manager - INFO - Writing results files.\n",
-      "2024-10-16 15:35:31,634 - directlfq.lfq_manager - INFO - Analysis finished!\n",
-      "2024-10-16 15:35:31,635 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
-      "2024-10-16 15:35:31,703 - directlfq.utils - INFO - using input type diann_peptide_based_on_precursor_ms1_and_ms2\n",
-      "2024-10-16 15:35:31,822 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
-      "2024-10-16 15:35:31,827 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
-      "2024-10-16 15:35:31,827 - directlfq.protein_intensity_estimation - INFO - 840 lfq-groups total\n",
-      "2024-10-16 15:35:32,152 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n",
-      "2024-10-16 15:35:32,173 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
-      "2024-10-16 15:35:32,237 - directlfq.protein_intensity_estimation - INFO - lfq-object 100\n",
-      "2024-10-16 15:35:32,298 - directlfq.protein_intensity_estimation - INFO - lfq-object 200\n",
-      "2024-10-16 15:35:32,443 - directlfq.protein_intensity_estimation - INFO - lfq-object 300\n",
-      "2024-10-16 15:35:32,492 - directlfq.protein_intensity_estimation - INFO - lfq-object 400\n",
-      "2024-10-16 15:35:32,554 - directlfq.protein_intensity_estimation - INFO - lfq-object 500\n",
-      "2024-10-16 15:35:32,609 - directlfq.protein_intensity_estimation - INFO - lfq-object 600\n",
-      "2024-10-16 15:35:32,710 - directlfq.protein_intensity_estimation - INFO - lfq-object 700\n",
-      "2024-10-16 15:35:32,771 - directlfq.protein_intensity_estimation - INFO - lfq-object 800\n",
-      "2024-10-16 15:35:32,976 - directlfq.lfq_manager - INFO - Writing results files.\n",
-      "2024-10-16 15:35:33,004 - directlfq.lfq_manager - INFO - Analysis finished!\n",
-      "2024-10-16 15:35:33,006 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
-      "2024-10-16 15:35:33,077 - directlfq.utils - INFO - using input type diann_precursor_ms1_and_ms2\n",
-      "2024-10-16 15:35:33,179 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
-      "2024-10-16 15:35:33,184 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
-      "2024-10-16 15:35:33,185 - directlfq.protein_intensity_estimation - INFO - 46 lfq-groups total\n",
-      "2024-10-16 15:35:33,280 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n",
-      "2024-10-16 15:35:33,289 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
-      "2024-10-16 15:35:33,610 - directlfq.lfq_manager - INFO - Writing results files.\n",
-      "2024-10-16 15:35:33,630 - directlfq.lfq_manager - INFO - Analysis finished!\n",
-      "2024-10-16 15:35:33,632 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
-      "2024-10-16 15:35:33,702 - directlfq.utils - INFO - using input type diann_precursor_ms1_and_ms2\n",
-      "2024-10-16 15:35:33,780 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
-      "2024-10-16 15:35:33,786 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
-      "2024-10-16 15:35:33,787 - directlfq.protein_intensity_estimation - INFO - 46 lfq-groups total\n",
-      "2024-10-16 15:35:33,885 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n",
-      "2024-10-16 15:35:33,895 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
-      "2024-10-16 15:35:34,274 - directlfq.lfq_manager - INFO - Could not add additional columns to protein table, printing without additional columns.\n",
-      "2024-10-16 15:35:34,275 - directlfq.lfq_manager - INFO - Writing results files.\n",
-      "2024-10-16 15:35:34,334 - directlfq.lfq_manager - INFO - Analysis finished!\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# run diann\n",
     "import directlfq.lfq_manager as lfq_manager\n",
@@ -152,25 +74,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "2024-10-16 15:35:34,343 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
-      "2024-10-16 15:35:34,488 - directlfq.utils - INFO - using input type maxquant_peptides_leading_razor_protein\n",
-      "2024-10-16 15:35:34,533 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
-      "2024-10-16 15:35:34,535 - directlfq.normalization - INFO - to few values for normalization without missing values. Including missing values\n",
-      "2024-10-16 15:35:34,541 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
-      "2024-10-16 15:35:34,542 - directlfq.protein_intensity_estimation - INFO - 49 lfq-groups total\n",
-      "2024-10-16 15:35:34,558 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
-      "2024-10-16 15:35:35,042 - directlfq.lfq_manager - INFO - Writing results files.\n",
-      "2024-10-16 15:35:35,054 - directlfq.lfq_manager - INFO - Analysis finished!\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "#run mq peptides\n",
     "\n",
@@ -186,35 +92,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "2024-10-16 15:35:35,061 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
-      "2024-10-16 15:35:35,240 - directlfq.utils - INFO - using input type maxquant_evidence_leading_razor_protein\n",
-      "2024-10-16 15:35:35,324 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
-      "2024-10-16 15:35:35,326 - directlfq.normalization - INFO - to few values for normalization without missing values. Including missing values\n",
-      "2024-10-16 15:35:35,332 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
-      "2024-10-16 15:35:35,332 - directlfq.protein_intensity_estimation - INFO - 50 lfq-groups total\n",
-      "2024-10-16 15:35:35,424 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n",
-      "2024-10-16 15:35:35,433 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
-      "2024-10-16 15:35:35,723 - directlfq.lfq_manager - INFO - Writing results files.\n",
-      "2024-10-16 15:35:35,738 - directlfq.lfq_manager - INFO - Analysis finished!\n",
-      "2024-10-16 15:35:35,739 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
-      "2024-10-16 15:35:35,875 - directlfq.utils - INFO - using input type maxquant_evidence_leading_razor_protein\n",
-      "2024-10-16 15:35:35,960 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
-      "2024-10-16 15:35:35,961 - root - INFO - Normalizing only selected proteins\n",
-      "2024-10-16 15:35:35,968 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
-      "2024-10-16 15:35:35,969 - directlfq.protein_intensity_estimation - INFO - 50 lfq-groups total\n",
-      "2024-10-16 15:35:35,986 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
-      "2024-10-16 15:35:36,558 - directlfq.lfq_manager - INFO - Writing results files.\n",
-      "2024-10-16 15:35:36,573 - directlfq.lfq_manager - INFO - Analysis finished!\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "#run mq evidence\n",
     "\n",
@@ -230,34 +110,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "2024-10-16 15:35:36,580 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
-      "2024-10-16 15:35:36,757 - directlfq.utils - INFO - using input type spectronaut_fragion_isotopes\n",
-      "2024-10-16 15:35:37,122 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
-      "2024-10-16 15:35:37,123 - root - INFO - Normalizing only selected proteins\n",
-      "2024-10-16 15:35:37,134 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
-      "2024-10-16 15:35:37,135 - directlfq.protein_intensity_estimation - INFO - 50 lfq-groups total\n",
-      "2024-10-16 15:35:37,155 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
-      "2024-10-16 15:35:38,484 - directlfq.lfq_manager - INFO - Writing results files.\n",
-      "2024-10-16 15:35:38,510 - directlfq.lfq_manager - INFO - Analysis finished!\n",
-      "2024-10-16 15:35:38,511 - directlfq.lfq_manager - INFO - Starting directLFQ analysis.\n",
-      "2024-10-16 15:35:38,648 - directlfq.utils - INFO - using input type spectronaut_fragion_isotopes\n",
-      "2024-10-16 15:35:39,003 - directlfq.lfq_manager - INFO - Performing sample normalization.\n",
-      "2024-10-16 15:35:39,011 - directlfq.lfq_manager - INFO - Estimating lfq intensities.\n",
-      "2024-10-16 15:35:39,012 - directlfq.protein_intensity_estimation - INFO - 50 lfq-groups total\n",
-      "2024-10-16 15:35:39,103 - directlfq.protein_intensity_estimation - INFO - using 10 processes\n",
-      "2024-10-16 15:35:39,111 - directlfq.protein_intensity_estimation - INFO - lfq-object 0\n",
-      "2024-10-16 15:35:39,539 - directlfq.lfq_manager - INFO - Writing results files.\n",
-      "2024-10-16 15:35:39,566 - directlfq.lfq_manager - INFO - Analysis finished!\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# run spectronaut\n",
     "import directlfq.lfq_manager as lfq_manager\n",