{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "d48b9454",
   "metadata": {},
   "source": [
    "# Protein Group readers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "3812811e",
   "metadata": {
    "tags": [
     "hide-cell"
    ]
   },
   "outputs": [],
   "source": [
    "%reload_ext autoreload \n",
    "%autoreload 2 "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "c0510071",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/lucas-diedrich/Documents/Projects/alphaX/alphabase/alphabase/alphabase/tools/data_downloader.py:4: DeprecationWarning: 'cgi' is deprecated and slated for removal in Python 3.13\n",
      "  import cgi\n",
      "/Users/lucas-diedrich/Documents/Projects/alphaX/alphabase/alphabase/alphabase/tools/data_downloader.py:18: ImportWarning: Dependency 'progressbar' not installed. Download progress will not be displayed.\n",
      "  warnings.warn(\n"
     ]
    }
   ],
   "source": [
    "# Helper packages\n",
    "import io\n",
    "from copy import copy\n",
    "from typing import Literal, Optional\n",
    "\n",
    "import anndata as ad\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "\n",
    "# alphabase\n",
    "from alphabase.pg_reader import pg_reader_provider\n",
    "from alphabase.tools.data_downloader import DataShareDownloader"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e17fe6eb",
   "metadata": {},
   "source": [
    "## Background \n",
    "\n",
    "The `alphabase.pg_reader` module provides a unifying interface **to read protein group (PG) tables** from different search engines and file formats. It is designed to be easy to use, and to provide a consistent output format in the form of `pandas.DataFrame`s, regardless of the input file format.\n",
    "\n",
    "### Introduction to protein group matrices\n",
    "\n",
    "Protein group matrices are the primary output for protein-level quantification in proteomics workflows. After search engines identify peptide spectrum matches (PSMs, see [PSM-reader tutorial](../nbs/psm_readers.ipynb)), they aggregate peptide-level evidence to infer protein-level abundances. These protein group tables represent a structured matrix that maps protein groups (features) to samples (observations), with estimated intensity values as entries.\n",
    "\n",
    "\n",
    "A minimal protein group table could look something like this:\n",
    "\n",
    "| proteins | sample_1 | sample_2 | sample_3 |\n",
    "|----------|----------|----------|----------|\n",
    "| P12345   | 1000.5   | 892.3    | 1150.7   |\n",
    "| Q67890   | 2500.1   | 2780.9   | 2340.2   |\n",
    "\n",
    "\n",
    "\n",
    "> 💡 Since some identified peptide sequences can match multiple proteins (such as isoforms or homologues), proteomics search engines typically handle this ambiguity by grouping these proteins into *protein groups* as features.\n",
    "\n",
    "\n",
    "In this example, protein P12345 has quantified intensities of 1000.5, 892.3, and 1150.7 in samples 1, 2, and 3 respectively.\n",
    "\n",
    "### Search engine outputs\n",
    "\n",
    "In reality, protein group tables are significantly more complex than this, as they contain additional feature-level information about the proteins (e.g., gene names, descriptions, alternative quantification methods), and the quantification (e.g., different intensity types like raw, LFQ quantification, iBAQ). This additional information can be valuable for downstream analyses, but also makes protein group tables a lot more difficult to work with, as the exact names and formats may differ between search engines, versions, and file formats.\n",
    "\n",
    "#### Unifying properties \n",
    "\n",
    "`alphabase` aligns the column names to a unified vocabulary, facilitating cross-engine comparisons. We can categorize protein group tables into several common types:\n",
    "\n",
    "**Type 1 — Minimal**: A basic features × samples matrix. Only intensity values are stored, with sample names as columns and protein groups as the index. *Example*: AlphaDIA.\n",
    "\n",
    "**Type 2 — Multiple Intensity Fields**: A wide matrix where each sample may appear multiple times with different quantification types (e.g., `SampleA_LFQ`, `SampleB_raw`). *Example*: AlphaPept.\n",
    "\n",
    "**Type 3 — Feature Metadata**: A features × samples matrix with one intensity value per sample, plus additional feature-level metadata columns (e.g., gene names, descriptions). *Example*: DIA-NN.\n",
    "\n",
    "**Type 4 — Combined**: A composite structure including both multiple intensity fields (Type 2) and feature-level metadata (Type 3). *Examples*: Spectronaut, MZTab, MaxQuant.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4547ae8c",
   "metadata": {},
   "source": [
    "## Code | Read and parse protein group tables\n",
    "\n",
    "The alphabase `pg_reader` module enables users to parse proteomics protein group reports to a dataframe for most common search engines with a single line of code via its `alphabase.pg_reader.pg_reader_provider` factory.\n",
    "\n",
    "\n",
    "All readers return a standardized pandas DataFrame with:\n",
    "- **Features as index**: Protein identifiers and metadata in the `pandas.DataFrame.Index`\n",
    "- **Samples as columns**: Sample/run identifiers as column index\n",
    "- **Intensity values**: Protein quantification data as `pandas.DataFrame.values`\n",
    "\n",
    "\n",
    "\n",
    "The readers **support different quantification methods** by matching regular expression patterns in the output tables and the **retrieval of desired metadata columns to standardized names**.\n",
    "\n",
    "\n",
    "The unified alphabase format enables seamless comparison and analysis across different search engines, facilitating:\n",
    "- Method comparison studies\n",
    "- Data integration workflows\n",
    "- Standardized downstream analysis pipelines"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a433a22a",
   "metadata": {},
   "source": [
    "### Available readers \n",
    "\n",
    "\n",
    "`alphabase.pg_reader.pg_reader_provider` has registered reader classes for the most common proteomics search engines. A list of implemented readers can be accessed via its `reader_dict` property:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "d7eeeefd",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Registered readers in alphabase:\n",
      "\t- alphadia\n",
      "\t- alphapept\n",
      "\t- diann\n",
      "\t- fragpipe\n",
      "\t- maxquant\n",
      "\t- mztab\n",
      "\t- spectronaut\n"
     ]
    }
   ],
   "source": [
    "all_registered_readers = pg_reader_provider.reader_dict.keys()\n",
    "\n",
    "# Display all registered readers\n",
    "sep = \"\\n\\t- \"\n",
    "print(\"Registered readers in alphabase:\", sep.join(sorted(all_registered_readers)), sep=sep)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d8352b39",
   "metadata": {},
   "source": [
    "### Interact with the reader provider"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "48b68899",
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_pg_matrix_example(output_dir: Optional[str] = None, search_engine: Literal[\"alphadia\", \"alphapept\", \"spectronaut\"] = \"alphadia\") -> str:\n",
    "    \"\"\"Get example data for the tutorial\n",
    "\n",
    "    The function downloads example data and stores it\n",
    "    in `output_dir`, or, alternatively in a temporary directory\n",
    "\n",
    "    Parameter\n",
    "    ---------\n",
    "    output_dir\n",
    "        Output directory. If `None`, creates a temporary directory\n",
    "\n",
    "    Returns\n",
    "    -------\n",
    "    File location\n",
    "    \"\"\"\n",
    "    EXAMPLE_URLS = {\n",
    "        \"alphadia\": \"https://datashare.biochem.mpg.de/s/4AtCZassaUzRR8K\",\n",
    "        \"alphapept\": \"https://datashare.biochem.mpg.de/s/6G6KHJqwcRPQiOO\",\n",
    "        \"spectronaut\": \"https://datashare.biochem.mpg.de/s/2u7U03wvmQDVT4y\",\n",
    "    }\n",
    "\n",
    "    if search_engine not in EXAMPLE_URLS:\n",
    "        raise KeyError(f\"{search_engine} not found, select one of {', '.join(EXAMPLE_URLS.keys())}\")\n",
    "\n",
    "    if output_dir is None:\n",
    "        from tempfile import tempdir\n",
    "\n",
    "        output_dir = tempdir\n",
    "\n",
    "    downloader = DataShareDownloader(url=EXAMPLE_URLS[search_engine], output_dir=output_dir)\n",
    "\n",
    "    return downloader.download()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dded4cee",
   "metadata": {},
   "source": [
    "### Example 1 - AlphaDIA\n",
    "\n",
    "We demonstrate how to interact with protein group tables via alphabase based on a minimal example output of the AlphaDIA search engine. \n",
    "\n",
    "First, let's get some minimal example data for the AlphaDIA output. The example data represents a DIA run of 6 HeLA samples on the Orbitrap Astral. \n",
    "\n",
    "You can see that the output data contains the feature names in the column `pg` and the computed protein group intensities per sample in the remaining columns.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "7f4bc10f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/var/folders/py/838_q5nd6594y27wbrpkhl3h0000gn/T/alphadia1.10.4__pg_matrix.tsv already exists (0.8597145080566406 MB)\n"
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       "                                pg  \\\n",
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       "...                                                 ...                   \n",
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       "0                                          0.000000e+00                   \n",
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       "...                                                 ...                   \n",
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       "\n",
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       "0                                          2.753702e+05                  \n",
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       "...                                                 ...                  \n",
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       "\n",
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       "...                                                 ...                 \n",
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       "\n",
       "[9364 rows x 7 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alphadia_example_path = get_pg_matrix_example(search_engine=\"alphadia\")\n",
    "\n",
    "# Parse with pandas for visualization purposes\n",
    "pd.read_csv(alphadia_example_path, sep=\"\\t\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a0ee852c",
   "metadata": {},
   "source": [
    "Then use the `pg_reader_provider.get_reader` method to get the AlphaDIA protein group reader. Use the `import_file` method to read the file, which is directly returned as a :class:`pandas.DataFrame`. \n",
    "\n",
    "Note how the dataframe values only contain the actual measurements and how the `pg` column was mapped to the standardized name `uniprot_ids`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "18fb6522",
   "metadata": {},
   "outputs": [
    {
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       "      <th>20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_03</th>\n",
       "      <th>20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_02</th>\n",
       "      <th>20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_01</th>\n",
       "      <th>20231023_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_after_03</th>\n",
       "      <th>20231023_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_after_02</th>\n",
       "      <th>20231023_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_after_01</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uniprot_ids</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>A0A024RBG1</th>\n",
       "      <td>5.597816e+05</td>\n",
       "      <td>6.285112e+05</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>3.153867e+05</td>\n",
       "      <td>2.753702e+05</td>\n",
       "      <td>4.505648e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A0A024RBG1;Q9NZJ9</th>\n",
       "      <td>1.331061e+06</td>\n",
       "      <td>1.400360e+06</td>\n",
       "      <td>1.551987e+06</td>\n",
       "      <td>1.606095e+06</td>\n",
       "      <td>1.464152e+06</td>\n",
       "      <td>1.397026e+06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A0A075B759;A0A075B767;P62937</th>\n",
       "      <td>2.024742e+08</td>\n",
       "      <td>8.552202e+06</td>\n",
       "      <td>1.837425e+08</td>\n",
       "      <td>1.674874e+08</td>\n",
       "      <td>1.768245e+08</td>\n",
       "      <td>1.595220e+08</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A0A096LP01</th>\n",
       "      <td>6.355092e+05</td>\n",
       "      <td>4.589410e+05</td>\n",
       "      <td>4.184495e+05</td>\n",
       "      <td>4.032932e+05</td>\n",
       "      <td>2.317467e+05</td>\n",
       "      <td>2.731363e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A0A096LP49</th>\n",
       "      <td>1.777069e+05</td>\n",
       "      <td>1.387537e+05</td>\n",
       "      <td>2.513601e+05</td>\n",
       "      <td>1.296699e+05</td>\n",
       "      <td>1.276095e+05</td>\n",
       "      <td>1.623200e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Q9Y6X3</th>\n",
       "      <td>3.898963e+05</td>\n",
       "      <td>4.353048e+05</td>\n",
       "      <td>4.150456e+05</td>\n",
       "      <td>5.069992e+05</td>\n",
       "      <td>4.195746e+05</td>\n",
       "      <td>3.675962e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Q9Y6X6</th>\n",
       "      <td>1.869312e+05</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>2.304623e+05</td>\n",
       "      <td>2.421623e+05</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Q9Y6X9</th>\n",
       "      <td>3.362758e+06</td>\n",
       "      <td>3.395221e+06</td>\n",
       "      <td>3.541975e+06</td>\n",
       "      <td>2.704210e+06</td>\n",
       "      <td>3.141519e+06</td>\n",
       "      <td>2.995787e+06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Q9Y6Y0</th>\n",
       "      <td>5.924220e+06</td>\n",
       "      <td>6.183842e+06</td>\n",
       "      <td>6.190598e+06</td>\n",
       "      <td>6.025724e+06</td>\n",
       "      <td>5.920595e+06</td>\n",
       "      <td>6.754984e+06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Q9Y6Y8</th>\n",
       "      <td>1.416146e+07</td>\n",
       "      <td>1.424916e+07</td>\n",
       "      <td>1.342342e+07</td>\n",
       "      <td>1.345135e+07</td>\n",
       "      <td>1.406395e+07</td>\n",
       "      <td>1.349913e+07</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>9364 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                              20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_03  \\\n",
       "uniprot_ids                                                                                       \n",
       "A0A024RBG1                                                         5.597816e+05                   \n",
       "A0A024RBG1;Q9NZJ9                                                  1.331061e+06                   \n",
       "A0A075B759;A0A075B767;P62937                                       2.024742e+08                   \n",
       "A0A096LP01                                                         6.355092e+05                   \n",
       "A0A096LP49                                                         1.777069e+05                   \n",
       "...                                                                         ...                   \n",
       "Q9Y6X3                                                             3.898963e+05                   \n",
       "Q9Y6X6                                                             1.869312e+05                   \n",
       "Q9Y6X9                                                             3.362758e+06                   \n",
       "Q9Y6Y0                                                             5.924220e+06                   \n",
       "Q9Y6Y8                                                             1.416146e+07                   \n",
       "\n",
       "                              20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_02  \\\n",
       "uniprot_ids                                                                                       \n",
       "A0A024RBG1                                                         6.285112e+05                   \n",
       "A0A024RBG1;Q9NZJ9                                                  1.400360e+06                   \n",
       "A0A075B759;A0A075B767;P62937                                       8.552202e+06                   \n",
       "A0A096LP01                                                         4.589410e+05                   \n",
       "A0A096LP49                                                         1.387537e+05                   \n",
       "...                                                                         ...                   \n",
       "Q9Y6X3                                                             4.353048e+05                   \n",
       "Q9Y6X6                                                             0.000000e+00                   \n",
       "Q9Y6X9                                                             3.395221e+06                   \n",
       "Q9Y6Y0                                                             6.183842e+06                   \n",
       "Q9Y6Y8                                                             1.424916e+07                   \n",
       "\n",
       "                              20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_01  \\\n",
       "uniprot_ids                                                                                       \n",
       "A0A024RBG1                                                         0.000000e+00                   \n",
       "A0A024RBG1;Q9NZJ9                                                  1.551987e+06                   \n",
       "A0A075B759;A0A075B767;P62937                                       1.837425e+08                   \n",
       "A0A096LP01                                                         4.184495e+05                   \n",
       "A0A096LP49                                                         2.513601e+05                   \n",
       "...                                                                         ...                   \n",
       "Q9Y6X3                                                             4.150456e+05                   \n",
       "Q9Y6X6                                                             0.000000e+00                   \n",
       "Q9Y6X9                                                             3.541975e+06                   \n",
       "Q9Y6Y0                                                             6.190598e+06                   \n",
       "Q9Y6Y8                                                             1.342342e+07                   \n",
       "\n",
       "                              20231023_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_after_03  \\\n",
       "uniprot_ids                                                                                      \n",
       "A0A024RBG1                                                         3.153867e+05                  \n",
       "A0A024RBG1;Q9NZJ9                                                  1.606095e+06                  \n",
       "A0A075B759;A0A075B767;P62937                                       1.674874e+08                  \n",
       "A0A096LP01                                                         4.032932e+05                  \n",
       "A0A096LP49                                                         1.296699e+05                  \n",
       "...                                                                         ...                  \n",
       "Q9Y6X3                                                             5.069992e+05                  \n",
       "Q9Y6X6                                                             2.304623e+05                  \n",
       "Q9Y6X9                                                             2.704210e+06                  \n",
       "Q9Y6Y0                                                             6.025724e+06                  \n",
       "Q9Y6Y8                                                             1.345135e+07                  \n",
       "\n",
       "                              20231023_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_after_02  \\\n",
       "uniprot_ids                                                                                      \n",
       "A0A024RBG1                                                         2.753702e+05                  \n",
       "A0A024RBG1;Q9NZJ9                                                  1.464152e+06                  \n",
       "A0A075B759;A0A075B767;P62937                                       1.768245e+08                  \n",
       "A0A096LP01                                                         2.317467e+05                  \n",
       "A0A096LP49                                                         1.276095e+05                  \n",
       "...                                                                         ...                  \n",
       "Q9Y6X3                                                             4.195746e+05                  \n",
       "Q9Y6X6                                                             2.421623e+05                  \n",
       "Q9Y6X9                                                             3.141519e+06                  \n",
       "Q9Y6Y0                                                             5.920595e+06                  \n",
       "Q9Y6Y8                                                             1.406395e+07                  \n",
       "\n",
       "                              20231023_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_after_01  \n",
       "uniprot_ids                                                                                     \n",
       "A0A024RBG1                                                         4.505648e+05                 \n",
       "A0A024RBG1;Q9NZJ9                                                  1.397026e+06                 \n",
       "A0A075B759;A0A075B767;P62937                                       1.595220e+08                 \n",
       "A0A096LP01                                                         2.731363e+05                 \n",
       "A0A096LP49                                                         1.623200e+05                 \n",
       "...                                                                         ...                 \n",
       "Q9Y6X3                                                             3.675962e+05                 \n",
       "Q9Y6X6                                                             0.000000e+00                 \n",
       "Q9Y6X9                                                             2.995787e+06                 \n",
       "Q9Y6Y0                                                             6.754984e+06                 \n",
       "Q9Y6Y8                                                             1.349913e+07                 \n",
       "\n",
       "[9364 rows x 6 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alphadia_reader = pg_reader_provider.get_reader('alphadia')\n",
    "\n",
    "# Import the file or a bytestream\n",
    "alphadia_report = alphadia_reader.import_file(alphadia_example_path)\n",
    "\n",
    "# Display the result\n",
    "alphadia_report"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fc3d5d90",
   "metadata": {},
   "source": [
    "### Example 2 - AlphaPept with different quantification methods\n",
    "\n",
    "AlphaPept is a DDA search engine that returns multiple quantification methods (raw intensities, LFQ) in its protein group report. We can use the reader to extract these different types of measurements by specifying the `measurement_regex` parameter.\n",
    "\n",
    "AlphaPept reports can be both in a `.hdf` or `.tsv` format. The `pg_readers` support all common data formats (text-based like `.tsv`, `.csv`, and binary like `.hdf` (via extra `alphabase[hdf]` dependency), `.parquet`) out of the box. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "48904224",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/var/folders/py/838_q5nd6594y27wbrpkhl3h0000gn/T/alphapept0.5.3__pg_matrix_csv.csv already exists (0.33005523681640625 MB)\n"
     ]
    },
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>A_LFQ</th>\n",
       "      <th>B_LFQ</th>\n",
       "      <th>A</th>\n",
       "      <th>B</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>sp|P36578|RL4_HUMAN</td>\n",
       "      <td>4.669329e+08</td>\n",
       "      <td>4.844083e+08</td>\n",
       "      <td>4.452735e+08</td>\n",
       "      <td>5.060678e+08</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>sp|Q9P258|RCC2_HUMAN</td>\n",
       "      <td>4.074842e+08</td>\n",
       "      <td>4.138132e+08</td>\n",
       "      <td>4.177856e+08</td>\n",
       "      <td>4.035118e+08</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>sp|O60518|RNBP6_HUMAN</td>\n",
       "      <td>4.960386e+06</td>\n",
       "      <td>2.022553e+06</td>\n",
       "      <td>1.295621e+06</td>\n",
       "      <td>5.687318e+06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>sp|P55036|PSMD4_HUMAN</td>\n",
       "      <td>1.157420e+08</td>\n",
       "      <td>1.123571e+08</td>\n",
       "      <td>1.130880e+08</td>\n",
       "      <td>1.150112e+08</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>sp|A1X283|SPD2B_HUMAN</td>\n",
       "      <td>1.247112e+07</td>\n",
       "      <td>1.180582e+07</td>\n",
       "      <td>1.380177e+07</td>\n",
       "      <td>1.047516e+07</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3776</th>\n",
       "      <td>sp|Q14966|ZN638_HUMAN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.139844e+06</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.139844e+06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3777</th>\n",
       "      <td>sp|P84095|RHOG_HUMAN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>9.466796e+05</td>\n",
       "      <td>NaN</td>\n",
       "      <td>9.466796e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3778</th>\n",
       "      <td>sp|Q99766|ATP5S_HUMAN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>3.577785e+05</td>\n",
       "      <td>NaN</td>\n",
       "      <td>3.577785e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3779</th>\n",
       "      <td>sp|O14925|TIM23_HUMAN,sp|Q5SRD1|TI23B_HUMAN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>9.237994e+05</td>\n",
       "      <td>NaN</td>\n",
       "      <td>9.237994e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3780</th>\n",
       "      <td>sp|P51946|CCNH_HUMAN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>9.278844e+05</td>\n",
       "      <td>NaN</td>\n",
       "      <td>9.278844e+05</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3781 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                       Unnamed: 0         A_LFQ         B_LFQ  \\\n",
       "0                             sp|P36578|RL4_HUMAN  4.669329e+08  4.844083e+08   \n",
       "1                            sp|Q9P258|RCC2_HUMAN  4.074842e+08  4.138132e+08   \n",
       "2                           sp|O60518|RNBP6_HUMAN  4.960386e+06  2.022553e+06   \n",
       "3                           sp|P55036|PSMD4_HUMAN  1.157420e+08  1.123571e+08   \n",
       "4                           sp|A1X283|SPD2B_HUMAN  1.247112e+07  1.180582e+07   \n",
       "...                                           ...           ...           ...   \n",
       "3776                        sp|Q14966|ZN638_HUMAN           NaN  1.139844e+06   \n",
       "3777                         sp|P84095|RHOG_HUMAN           NaN  9.466796e+05   \n",
       "3778                        sp|Q99766|ATP5S_HUMAN           NaN  3.577785e+05   \n",
       "3779  sp|O14925|TIM23_HUMAN,sp|Q5SRD1|TI23B_HUMAN           NaN  9.237994e+05   \n",
       "3780                         sp|P51946|CCNH_HUMAN           NaN  9.278844e+05   \n",
       "\n",
       "                 A             B  \n",
       "0     4.452735e+08  5.060678e+08  \n",
       "1     4.177856e+08  4.035118e+08  \n",
       "2     1.295621e+06  5.687318e+06  \n",
       "3     1.130880e+08  1.150112e+08  \n",
       "4     1.380177e+07  1.047516e+07  \n",
       "...            ...           ...  \n",
       "3776           NaN  1.139844e+06  \n",
       "3777           NaN  9.466796e+05  \n",
       "3778           NaN  3.577785e+05  \n",
       "3779           NaN  9.237994e+05  \n",
       "3780           NaN  9.278844e+05  \n",
       "\n",
       "[3781 rows x 5 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Create example MaxQuant data with multiple quantification types\n",
    "alphapept_example_path = get_pg_matrix_example(search_engine=\"alphapept\")\n",
    "pd.read_csv(alphapept_example_path)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d55ab6db",
   "metadata": {},
   "source": [
    "#### Default - raw intensities\n",
    "Let's first use the default option that imports raw intensities. You can see that the reader automatically extracts only raw intensity columns and that it parses the uniprot header index to a more streamlined format."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "a9fd0af3",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>proteins</th>\n",
       "      <th>uniprot_ids</th>\n",
       "      <th>ensembl_ids</th>\n",
       "      <th>source_db</th>\n",
       "      <th>is_decoy</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>RL4_HUMAN</th>\n",
       "      <th>P36578</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td>445273477.0318756</td>\n",
       "      <td>506067774.6891948</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>RCC2_HUMAN</th>\n",
       "      <th>Q9P258</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td>417785611.6324583</td>\n",
       "      <td>403511752.8857417</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>RNBP6_HUMAN</th>\n",
       "      <th>O60518</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td>1295621.2466679448</td>\n",
       "      <td>5687318.493374016</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PSMD4_HUMAN</th>\n",
       "      <th>P55036</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td>113087994.44403341</td>\n",
       "      <td>115011156.7335174</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SPD2B_HUMAN</th>\n",
       "      <th>A1X283</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td>13801771.733223092</td>\n",
       "      <td>10475164.42857083</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ZN638_HUMAN</th>\n",
       "      <th>Q14966</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td></td>\n",
       "      <td>1139843.6453892316</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>RHOG_HUMAN</th>\n",
       "      <th>P84095</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td></td>\n",
       "      <td>946679.6466570131</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ATP5S_HUMAN</th>\n",
       "      <th>Q99766</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td></td>\n",
       "      <td>357778.52002529387</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TIM23_HUMAN;TI23B_HUMAN</th>\n",
       "      <th>O14925;Q5SRD1</th>\n",
       "      <th>na;na</th>\n",
       "      <th>sp;sp</th>\n",
       "      <th>False</th>\n",
       "      <td></td>\n",
       "      <td>923799.3856913601</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CCNH_HUMAN</th>\n",
       "      <th>P51946</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td></td>\n",
       "      <td>927884.4020782198</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3781 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                                                       A  \\\n",
       "proteins                uniprot_ids   ensembl_ids source_db is_decoy                       \n",
       "RL4_HUMAN               P36578        na          sp        False      445273477.0318756   \n",
       "RCC2_HUMAN              Q9P258        na          sp        False      417785611.6324583   \n",
       "RNBP6_HUMAN             O60518        na          sp        False     1295621.2466679448   \n",
       "PSMD4_HUMAN             P55036        na          sp        False     113087994.44403341   \n",
       "SPD2B_HUMAN             A1X283        na          sp        False     13801771.733223092   \n",
       "...                                                                                  ...   \n",
       "ZN638_HUMAN             Q14966        na          sp        False                          \n",
       "RHOG_HUMAN              P84095        na          sp        False                          \n",
       "ATP5S_HUMAN             Q99766        na          sp        False                          \n",
       "TIM23_HUMAN;TI23B_HUMAN O14925;Q5SRD1 na;na       sp;sp     False                          \n",
       "CCNH_HUMAN              P51946        na          sp        False                          \n",
       "\n",
       "                                                                                       B  \n",
       "proteins                uniprot_ids   ensembl_ids source_db is_decoy                      \n",
       "RL4_HUMAN               P36578        na          sp        False      506067774.6891948  \n",
       "RCC2_HUMAN              Q9P258        na          sp        False      403511752.8857417  \n",
       "RNBP6_HUMAN             O60518        na          sp        False      5687318.493374016  \n",
       "PSMD4_HUMAN             P55036        na          sp        False      115011156.7335174  \n",
       "SPD2B_HUMAN             A1X283        na          sp        False      10475164.42857083  \n",
       "...                                                                                  ...  \n",
       "ZN638_HUMAN             Q14966        na          sp        False     1139843.6453892316  \n",
       "RHOG_HUMAN              P84095        na          sp        False      946679.6466570131  \n",
       "ATP5S_HUMAN             Q99766        na          sp        False     357778.52002529387  \n",
       "TIM23_HUMAN;TI23B_HUMAN O14925;Q5SRD1 na;na       sp;sp     False      923799.3856913601  \n",
       "CCNH_HUMAN              P51946        na          sp        False      927884.4020782198  \n",
       "\n",
       "[3781 rows x 2 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Default: raw intensities\n",
    "alphapept_reader_default = pg_reader_provider.get_reader('alphapept')\n",
    "alphapept_reader_default.import_file(alphapept_example_path)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3f0497c4",
   "metadata": {},
   "source": [
    "#### LFQ runs\n",
    "We can easily extract the LFQ intensities by selecting the pre-defined regular expression to extract them:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "35d8d28d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
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       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>A_LFQ</th>\n",
       "      <th>B_LFQ</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proteins</th>\n",
       "      <th>uniprot_ids</th>\n",
       "      <th>ensembl_ids</th>\n",
       "      <th>source_db</th>\n",
       "      <th>is_decoy</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>RL4_HUMAN</th>\n",
       "      <th>P36578</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td>466932936.27537036</td>\n",
       "      <td>484408315.44570005</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>RCC2_HUMAN</th>\n",
       "      <th>Q9P258</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td>407484183.9302226</td>\n",
       "      <td>413813180.5879775</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>RNBP6_HUMAN</th>\n",
       "      <th>O60518</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td>4960386.374516514</td>\n",
       "      <td>2022553.3655254466</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PSMD4_HUMAN</th>\n",
       "      <th>P55036</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td>115742020.94987468</td>\n",
       "      <td>112357130.22767611</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SPD2B_HUMAN</th>\n",
       "      <th>A1X283</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td>12471120.728621317</td>\n",
       "      <td>11805815.433172602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ZN638_HUMAN</th>\n",
       "      <th>Q14966</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td></td>\n",
       "      <td>1139843.6453892316</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>RHOG_HUMAN</th>\n",
       "      <th>P84095</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td></td>\n",
       "      <td>946679.6466570131</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ATP5S_HUMAN</th>\n",
       "      <th>Q99766</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td></td>\n",
       "      <td>357778.52002529387</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TIM23_HUMAN;TI23B_HUMAN</th>\n",
       "      <th>O14925;Q5SRD1</th>\n",
       "      <th>na;na</th>\n",
       "      <th>sp;sp</th>\n",
       "      <th>False</th>\n",
       "      <td></td>\n",
       "      <td>923799.3856913601</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CCNH_HUMAN</th>\n",
       "      <th>P51946</th>\n",
       "      <th>na</th>\n",
       "      <th>sp</th>\n",
       "      <th>False</th>\n",
       "      <td></td>\n",
       "      <td>927884.4020782198</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3781 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                                                   A_LFQ  \\\n",
       "proteins                uniprot_ids   ensembl_ids source_db is_decoy                       \n",
       "RL4_HUMAN               P36578        na          sp        False     466932936.27537036   \n",
       "RCC2_HUMAN              Q9P258        na          sp        False      407484183.9302226   \n",
       "RNBP6_HUMAN             O60518        na          sp        False      4960386.374516514   \n",
       "PSMD4_HUMAN             P55036        na          sp        False     115742020.94987468   \n",
       "SPD2B_HUMAN             A1X283        na          sp        False     12471120.728621317   \n",
       "...                                                                                  ...   \n",
       "ZN638_HUMAN             Q14966        na          sp        False                          \n",
       "RHOG_HUMAN              P84095        na          sp        False                          \n",
       "ATP5S_HUMAN             Q99766        na          sp        False                          \n",
       "TIM23_HUMAN;TI23B_HUMAN O14925;Q5SRD1 na;na       sp;sp     False                          \n",
       "CCNH_HUMAN              P51946        na          sp        False                          \n",
       "\n",
       "                                                                                   B_LFQ  \n",
       "proteins                uniprot_ids   ensembl_ids source_db is_decoy                      \n",
       "RL4_HUMAN               P36578        na          sp        False     484408315.44570005  \n",
       "RCC2_HUMAN              Q9P258        na          sp        False      413813180.5879775  \n",
       "RNBP6_HUMAN             O60518        na          sp        False     2022553.3655254466  \n",
       "PSMD4_HUMAN             P55036        na          sp        False     112357130.22767611  \n",
       "SPD2B_HUMAN             A1X283        na          sp        False     11805815.433172602  \n",
       "...                                                                                  ...  \n",
       "ZN638_HUMAN             Q14966        na          sp        False     1139843.6453892316  \n",
       "RHOG_HUMAN              P84095        na          sp        False      946679.6466570131  \n",
       "ATP5S_HUMAN             Q99766        na          sp        False     357778.52002529387  \n",
       "TIM23_HUMAN;TI23B_HUMAN O14925;Q5SRD1 na;na       sp;sp     False      923799.3856913601  \n",
       "CCNH_HUMAN              P51946        na          sp        False      927884.4020782198  \n",
       "\n",
       "[3781 rows x 2 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# LFQ intensities\n",
    "alphapept_reader_lfq = pg_reader_provider.get_reader('alphapept', measurement_regex=\"lfq\")\n",
    "alphapept_reader_lfq.import_file(alphapept_example_path)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ddef95cd",
   "metadata": {},
   "source": [
    "#### Explore all pre-configured patterns\n",
    "\n",
    "You can also pass custom patterns as valid regular expression and check out all pre-configured regular expression sets with the `get_preconfigured_regex` method:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "3681a6ac",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'raw': '^.*(?<!_LFQ)$', 'lfq': '_LFQ$'}"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alphapept_reader_default.get_preconfigured_regex()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2e5158c2",
   "metadata": {},
   "source": [
    "### Example 3 - Spectronaut reports\n",
    "\n",
    "Next, we explore how users can extract non-standard columns to a unified vocabulary based on a Spectronaut PG report. Spectronaut allows users to flexibly export custom feature-level metadata. `alphabase` allows users to extract this metadata by adding new columns to the streamlined column mapping."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "472ee22e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/var/folders/py/838_q5nd6594y27wbrpkhl3h0000gn/T/olsen-wide-format-site-report.tsv does not yet exist\n",
      "/var/folders/py/838_q5nd6594y27wbrpkhl3h0000gn/T/olsen-wide-format-site-report.tsv successfully downloaded (27.531264305114746 MB)\n"
     ]
    },
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>PG.Genes</th>\n",
       "      <th>PG.Organisms</th>\n",
       "      <th>PG.ProteinNames</th>\n",
       "      <th>PTM.CollapseKey</th>\n",
       "      <th>PTM.FlankingRegion</th>\n",
       "      <th>PTM.ModificationTitle</th>\n",
       "      <th>PTM.Multiplicity</th>\n",
       "      <th>PTM.ProteinId</th>\n",
       "      <th>PTM.SiteAA</th>\n",
       "      <th>PTM.SiteLocation</th>\n",
       "      <th>...</th>\n",
       "      <th>[27] 20180816_QE3_nLC3_AH_DIA_H100_Y25_03.raw.PTM.Quantity</th>\n",
       "      <th>[28] 20180816_QE3_nLC3_AH_DIA_H100_Y25_04.raw.PTM.Quantity</th>\n",
       "      <th>[29] 20180816_QE3_nLC3_AH_DIA_H100_Y25_05.raw.PTM.Quantity</th>\n",
       "      <th>[30] 20180816_QE3_nLC3_AH_DIA_H100_Y25_06.raw.PTM.Quantity</th>\n",
       "      <th>[31] 20180816_QE3_nLC3_AH_DIA_H100_Y50_01.raw.PTM.Quantity</th>\n",
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       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TRBV19;TRB</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>TVB19_HUMAN;TRBR1_HUMAN</td>\n",
       "      <td>A0A075B6N1_S86_M3</td>\n",
       "      <td>IAEGYSVSREKKESF</td>\n",
       "      <td>Phospho (STY)</td>\n",
       "      <td>3</td>\n",
       "      <td>A0A075B6N1</td>\n",
       "      <td>S</td>\n",
       "      <td>86</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.8359375</td>\n",
       "      <td>103632.6015625</td>\n",
       "      <td>90488.9296875</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.2734375</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.2734375</td>\n",
       "      <td>109199.875</td>\n",
       "      <td>112307.4765625</td>\n",
       "      <td>112374.84375</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TRBV19;TRB</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>TVB19_HUMAN;TRBR1_HUMAN</td>\n",
       "      <td>A0A075B6N1_S84_M3</td>\n",
       "      <td>GDIAEGYSVSREKKE</td>\n",
       "      <td>Phospho (STY)</td>\n",
       "      <td>3</td>\n",
       "      <td>A0A075B6N1</td>\n",
       "      <td>S</td>\n",
       "      <td>84</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.8359375</td>\n",
       "      <td>103632.6015625</td>\n",
       "      <td>90488.9296875</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.2734375</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.2734375</td>\n",
       "      <td>109199.875</td>\n",
       "      <td>112307.4765625</td>\n",
       "      <td>112374.84375</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TRBV19;TRB</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>TVB19_HUMAN;TRBR1_HUMAN</td>\n",
       "      <td>A0A075B6N1_Y83_M3</td>\n",
       "      <td>KGDIAEGYSVSREKK</td>\n",
       "      <td>Phospho (STY)</td>\n",
       "      <td>3</td>\n",
       "      <td>A0A075B6N1</td>\n",
       "      <td>Y</td>\n",
       "      <td>83</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.8359375</td>\n",
       "      <td>103632.6015625</td>\n",
       "      <td>90488.9296875</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.2734375</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.2734375</td>\n",
       "      <td>109199.875</td>\n",
       "      <td>112307.4765625</td>\n",
       "      <td>112374.84375</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TRBV19;TRB</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>TVB19_HUMAN;TRBR1_HUMAN</td>\n",
       "      <td>P0DSE2_S86_M3</td>\n",
       "      <td>IAEGYSVSREKKESF</td>\n",
       "      <td>Phospho (STY)</td>\n",
       "      <td>3</td>\n",
       "      <td>P0DSE2</td>\n",
       "      <td>S</td>\n",
       "      <td>86</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.8359375</td>\n",
       "      <td>103632.6015625</td>\n",
       "      <td>90488.9296875</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.2734375</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.2734375</td>\n",
       "      <td>109199.875</td>\n",
       "      <td>112307.4765625</td>\n",
       "      <td>112374.84375</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>TRBV19;TRB</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>TVB19_HUMAN;TRBR1_HUMAN</td>\n",
       "      <td>P0DSE2_S84_M3</td>\n",
       "      <td>GDIAEGYSVSREKKE</td>\n",
       "      <td>Phospho (STY)</td>\n",
       "      <td>3</td>\n",
       "      <td>P0DSE2</td>\n",
       "      <td>S</td>\n",
       "      <td>84</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.8359375</td>\n",
       "      <td>103632.6015625</td>\n",
       "      <td>90488.9296875</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.2734375</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.2734375</td>\n",
       "      <td>109199.875</td>\n",
       "      <td>112307.4765625</td>\n",
       "      <td>112374.84375</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54858</th>\n",
       "      <td>MORC2</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>MORC2_HUMAN</td>\n",
       "      <td>Q9Y6X9_S739_M2</td>\n",
       "      <td>ATPSRKRSVAVSDEE</td>\n",
       "      <td>Phospho (STY)</td>\n",
       "      <td>2</td>\n",
       "      <td>Q9Y6X9</td>\n",
       "      <td>S</td>\n",
       "      <td>739</td>\n",
       "      <td>...</td>\n",
       "      <td>23552.466796875</td>\n",
       "      <td>22144.580078125</td>\n",
       "      <td>20846.8515625</td>\n",
       "      <td>24248.41796875</td>\n",
       "      <td>22490.0546875</td>\n",
       "      <td>22095.990234375</td>\n",
       "      <td>25553.849609375</td>\n",
       "      <td>22250.546875</td>\n",
       "      <td>14592.869140625</td>\n",
       "      <td>19265.998046875</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54859</th>\n",
       "      <td>MORC2</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>MORC2_HUMAN</td>\n",
       "      <td>Q9Y6X9-2_S681_M2</td>\n",
       "      <td>RKRSVAVSDEEEVEE</td>\n",
       "      <td>Phospho (STY)</td>\n",
       "      <td>2</td>\n",
       "      <td>Q9Y6X9-2</td>\n",
       "      <td>S</td>\n",
       "      <td>681</td>\n",
       "      <td>...</td>\n",
       "      <td>23552.466796875</td>\n",
       "      <td>22144.580078125</td>\n",
       "      <td>20846.8515625</td>\n",
       "      <td>24248.41796875</td>\n",
       "      <td>22490.0546875</td>\n",
       "      <td>22095.990234375</td>\n",
       "      <td>25553.849609375</td>\n",
       "      <td>22250.546875</td>\n",
       "      <td>14592.869140625</td>\n",
       "      <td>19265.998046875</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54860</th>\n",
       "      <td>MORC2</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>MORC2_HUMAN</td>\n",
       "      <td>Q9Y6X9-2_S677_M2</td>\n",
       "      <td>ATPSRKRSVAVSDEE</td>\n",
       "      <td>Phospho (STY)</td>\n",
       "      <td>2</td>\n",
       "      <td>Q9Y6X9-2</td>\n",
       "      <td>S</td>\n",
       "      <td>677</td>\n",
       "      <td>...</td>\n",
       "      <td>23552.466796875</td>\n",
       "      <td>22144.580078125</td>\n",
       "      <td>20846.8515625</td>\n",
       "      <td>24248.41796875</td>\n",
       "      <td>22490.0546875</td>\n",
       "      <td>22095.990234375</td>\n",
       "      <td>25553.849609375</td>\n",
       "      <td>22250.546875</td>\n",
       "      <td>14592.869140625</td>\n",
       "      <td>19265.998046875</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54861</th>\n",
       "      <td>IVNS1ABP</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>NS1BP_HUMAN</td>\n",
       "      <td>Q9Y6Y0_M341_M1</td>\n",
       "      <td>SKSLSFEMQQDELIE</td>\n",
       "      <td>Oxidation (M)</td>\n",
       "      <td>1</td>\n",
       "      <td>Q9Y6Y0</td>\n",
       "      <td>M</td>\n",
       "      <td>341</td>\n",
       "      <td>...</td>\n",
       "      <td>Filtered</td>\n",
       "      <td>17287.40625</td>\n",
       "      <td>Filtered</td>\n",
       "      <td>15751.861328125</td>\n",
       "      <td>14749.724609375</td>\n",
       "      <td>12410.79296875</td>\n",
       "      <td>14130.1396484375</td>\n",
       "      <td>Filtered</td>\n",
       "      <td>13198.474609375</td>\n",
       "      <td>13553.0908203125</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54862</th>\n",
       "      <td>IVNS1ABP</td>\n",
       "      <td>Homo sapiens</td>\n",
       "      <td>NS1BP_HUMAN</td>\n",
       "      <td>Q9Y6Y0_S338_M1</td>\n",
       "      <td>PKLSKSLSFEMQQDE</td>\n",
       "      <td>Phospho (STY)</td>\n",
       "      <td>1</td>\n",
       "      <td>Q9Y6Y0</td>\n",
       "      <td>S</td>\n",
       "      <td>338</td>\n",
       "      <td>...</td>\n",
       "      <td>Filtered</td>\n",
       "      <td>17287.40625</td>\n",
       "      <td>Filtered</td>\n",
       "      <td>15751.861328125</td>\n",
       "      <td>14749.724609375</td>\n",
       "      <td>12410.79296875</td>\n",
       "      <td>14130.1396484375</td>\n",
       "      <td>7562.62060546875</td>\n",
       "      <td>13198.474609375</td>\n",
       "      <td>13553.0908203125</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>54863 rows × 46 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         PG.Genes  PG.Organisms          PG.ProteinNames    PTM.CollapseKey  \\\n",
       "0      TRBV19;TRB  Homo sapiens  TVB19_HUMAN;TRBR1_HUMAN  A0A075B6N1_S86_M3   \n",
       "1      TRBV19;TRB  Homo sapiens  TVB19_HUMAN;TRBR1_HUMAN  A0A075B6N1_S84_M3   \n",
       "2      TRBV19;TRB  Homo sapiens  TVB19_HUMAN;TRBR1_HUMAN  A0A075B6N1_Y83_M3   \n",
       "3      TRBV19;TRB  Homo sapiens  TVB19_HUMAN;TRBR1_HUMAN      P0DSE2_S86_M3   \n",
       "4      TRBV19;TRB  Homo sapiens  TVB19_HUMAN;TRBR1_HUMAN      P0DSE2_S84_M3   \n",
       "...           ...           ...                      ...                ...   \n",
       "54858       MORC2  Homo sapiens              MORC2_HUMAN     Q9Y6X9_S739_M2   \n",
       "54859       MORC2  Homo sapiens              MORC2_HUMAN   Q9Y6X9-2_S681_M2   \n",
       "54860       MORC2  Homo sapiens              MORC2_HUMAN   Q9Y6X9-2_S677_M2   \n",
       "54861    IVNS1ABP  Homo sapiens              NS1BP_HUMAN     Q9Y6Y0_M341_M1   \n",
       "54862    IVNS1ABP  Homo sapiens              NS1BP_HUMAN     Q9Y6Y0_S338_M1   \n",
       "\n",
       "      PTM.FlankingRegion PTM.ModificationTitle  PTM.Multiplicity  \\\n",
       "0        IAEGYSVSREKKESF         Phospho (STY)                 3   \n",
       "1        GDIAEGYSVSREKKE         Phospho (STY)                 3   \n",
       "2        KGDIAEGYSVSREKK         Phospho (STY)                 3   \n",
       "3        IAEGYSVSREKKESF         Phospho (STY)                 3   \n",
       "4        GDIAEGYSVSREKKE         Phospho (STY)                 3   \n",
       "...                  ...                   ...               ...   \n",
       "54858    ATPSRKRSVAVSDEE         Phospho (STY)                 2   \n",
       "54859    RKRSVAVSDEEEVEE         Phospho (STY)                 2   \n",
       "54860    ATPSRKRSVAVSDEE         Phospho (STY)                 2   \n",
       "54861    SKSLSFEMQQDELIE         Oxidation (M)                 1   \n",
       "54862    PKLSKSLSFEMQQDE         Phospho (STY)                 1   \n",
       "\n",
       "      PTM.ProteinId PTM.SiteAA  PTM.SiteLocation  ...  \\\n",
       "0        A0A075B6N1          S                86  ...   \n",
       "1        A0A075B6N1          S                84  ...   \n",
       "2        A0A075B6N1          Y                83  ...   \n",
       "3            P0DSE2          S                86  ...   \n",
       "4            P0DSE2          S                84  ...   \n",
       "...             ...        ...               ...  ...   \n",
       "54858        Q9Y6X9          S               739  ...   \n",
       "54859      Q9Y6X9-2          S               681  ...   \n",
       "54860      Q9Y6X9-2          S               677  ...   \n",
       "54861        Q9Y6Y0          M               341  ...   \n",
       "54862        Q9Y6Y0          S               338  ...   \n",
       "\n",
       "      [27] 20180816_QE3_nLC3_AH_DIA_H100_Y25_03.raw.PTM.Quantity  \\\n",
       "0                                          69968.8359375           \n",
       "1                                          69968.8359375           \n",
       "2                                          69968.8359375           \n",
       "3                                          69968.8359375           \n",
       "4                                          69968.8359375           \n",
       "...                                                  ...           \n",
       "54858                                    23552.466796875           \n",
       "54859                                    23552.466796875           \n",
       "54860                                    23552.466796875           \n",
       "54861                                           Filtered           \n",
       "54862                                           Filtered           \n",
       "\n",
       "      [28] 20180816_QE3_nLC3_AH_DIA_H100_Y25_04.raw.PTM.Quantity  \\\n",
       "0                                         103632.6015625           \n",
       "1                                         103632.6015625           \n",
       "2                                         103632.6015625           \n",
       "3                                         103632.6015625           \n",
       "4                                         103632.6015625           \n",
       "...                                                  ...           \n",
       "54858                                    22144.580078125           \n",
       "54859                                    22144.580078125           \n",
       "54860                                    22144.580078125           \n",
       "54861                                        17287.40625           \n",
       "54862                                        17287.40625           \n",
       "\n",
       "      [29] 20180816_QE3_nLC3_AH_DIA_H100_Y25_05.raw.PTM.Quantity  \\\n",
       "0                                          90488.9296875           \n",
       "1                                          90488.9296875           \n",
       "2                                          90488.9296875           \n",
       "3                                          90488.9296875           \n",
       "4                                          90488.9296875           \n",
       "...                                                  ...           \n",
       "54858                                      20846.8515625           \n",
       "54859                                      20846.8515625           \n",
       "54860                                      20846.8515625           \n",
       "54861                                           Filtered           \n",
       "54862                                           Filtered           \n",
       "\n",
       "      [30] 20180816_QE3_nLC3_AH_DIA_H100_Y25_06.raw.PTM.Quantity  \\\n",
       "0                                          113429.859375           \n",
       "1                                          113429.859375           \n",
       "2                                          113429.859375           \n",
       "3                                          113429.859375           \n",
       "4                                          113429.859375           \n",
       "...                                                  ...           \n",
       "54858                                     24248.41796875           \n",
       "54859                                     24248.41796875           \n",
       "54860                                     24248.41796875           \n",
       "54861                                    15751.861328125           \n",
       "54862                                    15751.861328125           \n",
       "\n",
       "      [31] 20180816_QE3_nLC3_AH_DIA_H100_Y50_01.raw.PTM.Quantity  \\\n",
       "0                                          96970.2734375           \n",
       "1                                          96970.2734375           \n",
       "2                                          96970.2734375           \n",
       "3                                          96970.2734375           \n",
       "4                                          96970.2734375           \n",
       "...                                                  ...           \n",
       "54858                                      22490.0546875           \n",
       "54859                                      22490.0546875           \n",
       "54860                                      22490.0546875           \n",
       "54861                                    14749.724609375           \n",
       "54862                                    14749.724609375           \n",
       "\n",
       "      [32] 20180816_QE3_nLC3_AH_DIA_H100_Y50_02.raw.PTM.Quantity  \\\n",
       "0                                           61069.171875           \n",
       "1                                           61069.171875           \n",
       "2                                           61069.171875           \n",
       "3                                           61069.171875           \n",
       "4                                           61069.171875           \n",
       "...                                                  ...           \n",
       "54858                                    22095.990234375           \n",
       "54859                                    22095.990234375           \n",
       "54860                                    22095.990234375           \n",
       "54861                                     12410.79296875           \n",
       "54862                                     12410.79296875           \n",
       "\n",
       "      [33] 20180816_QE3_nLC3_AH_DIA_H100_Y50_03.raw.PTM.Quantity  \\\n",
       "0                                          99673.2734375           \n",
       "1                                          99673.2734375           \n",
       "2                                          99673.2734375           \n",
       "3                                          99673.2734375           \n",
       "4                                          99673.2734375           \n",
       "...                                                  ...           \n",
       "54858                                    25553.849609375           \n",
       "54859                                    25553.849609375           \n",
       "54860                                    25553.849609375           \n",
       "54861                                   14130.1396484375           \n",
       "54862                                   14130.1396484375           \n",
       "\n",
       "      [34] 20180816_QE3_nLC3_AH_DIA_H100_Y50_04.raw.PTM.Quantity  \\\n",
       "0                                             109199.875           \n",
       "1                                             109199.875           \n",
       "2                                             109199.875           \n",
       "3                                             109199.875           \n",
       "4                                             109199.875           \n",
       "...                                                  ...           \n",
       "54858                                       22250.546875           \n",
       "54859                                       22250.546875           \n",
       "54860                                       22250.546875           \n",
       "54861                                           Filtered           \n",
       "54862                                   7562.62060546875           \n",
       "\n",
       "      [35] 20180816_QE3_nLC3_AH_DIA_H100_Y50_05.raw.PTM.Quantity  \\\n",
       "0                                         112307.4765625           \n",
       "1                                         112307.4765625           \n",
       "2                                         112307.4765625           \n",
       "3                                         112307.4765625           \n",
       "4                                         112307.4765625           \n",
       "...                                                  ...           \n",
       "54858                                    14592.869140625           \n",
       "54859                                    14592.869140625           \n",
       "54860                                    14592.869140625           \n",
       "54861                                    13198.474609375           \n",
       "54862                                    13198.474609375           \n",
       "\n",
       "      [36] 20180816_QE3_nLC3_AH_DIA_H100_Y50_06.raw.PTM.Quantity  \n",
       "0                                           112374.84375          \n",
       "1                                           112374.84375          \n",
       "2                                           112374.84375          \n",
       "3                                           112374.84375          \n",
       "4                                           112374.84375          \n",
       "...                                                  ...          \n",
       "54858                                    19265.998046875          \n",
       "54859                                    19265.998046875          \n",
       "54860                                    19265.998046875          \n",
       "54861                                   13553.0908203125          \n",
       "54862                                   13553.0908203125          \n",
       "\n",
       "[54863 rows x 46 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "spectronaut_example_path = get_pg_matrix_example(search_engine=\"spectronaut\")\n",
    "\n",
    "# Parse with pandas for visualization purposes\n",
    "pd.read_csv(spectronaut_example_path, sep=\"\\t\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e3c63473",
   "metadata": {},
   "source": [
    "The default reader extracts some streamlined information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "53449c57",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>[7] 20180816_QE3_nLC3_AH_DIA_H100_Y100_01.raw.PTM.Quantity</th>\n",
       "      <th>[8] 20180816_QE3_nLC3_AH_DIA_H100_Y100_02.raw.PTM.Quantity</th>\n",
       "      <th>[9] 20180816_QE3_nLC3_AH_DIA_H100_Y100_03.raw.PTM.Quantity</th>\n",
       "      <th>[10] 20180816_QE3_nLC3_AH_DIA_H100_Y100_04.raw.PTM.Quantity</th>\n",
       "      <th>...</th>\n",
       "      <th>[27] 20180816_QE3_nLC3_AH_DIA_H100_Y25_03.raw.PTM.Quantity</th>\n",
       "      <th>[28] 20180816_QE3_nLC3_AH_DIA_H100_Y25_04.raw.PTM.Quantity</th>\n",
       "      <th>[29] 20180816_QE3_nLC3_AH_DIA_H100_Y25_05.raw.PTM.Quantity</th>\n",
       "      <th>[30] 20180816_QE3_nLC3_AH_DIA_H100_Y25_06.raw.PTM.Quantity</th>\n",
       "      <th>[31] 20180816_QE3_nLC3_AH_DIA_H100_Y50_01.raw.PTM.Quantity</th>\n",
       "      <th>[32] 20180816_QE3_nLC3_AH_DIA_H100_Y50_02.raw.PTM.Quantity</th>\n",
       "      <th>[33] 20180816_QE3_nLC3_AH_DIA_H100_Y50_03.raw.PTM.Quantity</th>\n",
       "      <th>[34] 20180816_QE3_nLC3_AH_DIA_H100_Y50_04.raw.PTM.Quantity</th>\n",
       "      <th>[35] 20180816_QE3_nLC3_AH_DIA_H100_Y50_05.raw.PTM.Quantity</th>\n",
       "      <th>[36] 20180816_QE3_nLC3_AH_DIA_H100_Y50_06.raw.PTM.Quantity</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proteins</th>\n",
       "      <th>genes</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th rowspan=\"5\" valign=\"top\">TVB19_HUMAN;TRBR1_HUMAN</th>\n",
       "      <th>TRBV19;TRB</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>89374.656250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>90181.578125</td>\n",
       "      <td>96197.070312</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.835938</td>\n",
       "      <td>103632.601562</td>\n",
       "      <td>90488.929688</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.273438</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.273438</td>\n",
       "      <td>109199.875000</td>\n",
       "      <td>112307.476562</td>\n",
       "      <td>112374.843750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TRBV19;TRB</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>89374.656250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>90181.578125</td>\n",
       "      <td>96197.070312</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.835938</td>\n",
       "      <td>103632.601562</td>\n",
       "      <td>90488.929688</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.273438</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.273438</td>\n",
       "      <td>109199.875000</td>\n",
       "      <td>112307.476562</td>\n",
       "      <td>112374.843750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TRBV19;TRB</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>89374.656250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>90181.578125</td>\n",
       "      <td>96197.070312</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.835938</td>\n",
       "      <td>103632.601562</td>\n",
       "      <td>90488.929688</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.273438</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.273438</td>\n",
       "      <td>109199.875000</td>\n",
       "      <td>112307.476562</td>\n",
       "      <td>112374.843750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TRBV19;TRB</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>89374.656250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>90181.578125</td>\n",
       "      <td>96197.070312</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.835938</td>\n",
       "      <td>103632.601562</td>\n",
       "      <td>90488.929688</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.273438</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.273438</td>\n",
       "      <td>109199.875000</td>\n",
       "      <td>112307.476562</td>\n",
       "      <td>112374.843750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TRBV19;TRB</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>89374.656250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>90181.578125</td>\n",
       "      <td>96197.070312</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.835938</td>\n",
       "      <td>103632.601562</td>\n",
       "      <td>90488.929688</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.273438</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.273438</td>\n",
       "      <td>109199.875000</td>\n",
       "      <td>112307.476562</td>\n",
       "      <td>112374.843750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"3\" valign=\"top\">MORC2_HUMAN</th>\n",
       "      <th>MORC2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6817.745605</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>18010.679688</td>\n",
       "      <td>12501.521484</td>\n",
       "      <td>17377.408203</td>\n",
       "      <td>13730.358398</td>\n",
       "      <td>...</td>\n",
       "      <td>23552.466797</td>\n",
       "      <td>22144.580078</td>\n",
       "      <td>20846.851562</td>\n",
       "      <td>24248.417969</td>\n",
       "      <td>22490.054688</td>\n",
       "      <td>22095.990234</td>\n",
       "      <td>25553.849609</td>\n",
       "      <td>22250.546875</td>\n",
       "      <td>14592.869141</td>\n",
       "      <td>19265.998047</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MORC2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6817.745605</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>18010.679688</td>\n",
       "      <td>12501.521484</td>\n",
       "      <td>17377.408203</td>\n",
       "      <td>13730.358398</td>\n",
       "      <td>...</td>\n",
       "      <td>23552.466797</td>\n",
       "      <td>22144.580078</td>\n",
       "      <td>20846.851562</td>\n",
       "      <td>24248.417969</td>\n",
       "      <td>22490.054688</td>\n",
       "      <td>22095.990234</td>\n",
       "      <td>25553.849609</td>\n",
       "      <td>22250.546875</td>\n",
       "      <td>14592.869141</td>\n",
       "      <td>19265.998047</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MORC2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6817.745605</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>18010.679688</td>\n",
       "      <td>12501.521484</td>\n",
       "      <td>17377.408203</td>\n",
       "      <td>13730.358398</td>\n",
       "      <td>...</td>\n",
       "      <td>23552.466797</td>\n",
       "      <td>22144.580078</td>\n",
       "      <td>20846.851562</td>\n",
       "      <td>24248.417969</td>\n",
       "      <td>22490.054688</td>\n",
       "      <td>22095.990234</td>\n",
       "      <td>25553.849609</td>\n",
       "      <td>22250.546875</td>\n",
       "      <td>14592.869141</td>\n",
       "      <td>19265.998047</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"2\" valign=\"top\">NS1BP_HUMAN</th>\n",
       "      <th>IVNS1ABP</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>38411.285156</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10104.601562</td>\n",
       "      <td>12773.764648</td>\n",
       "      <td>10412.311523</td>\n",
       "      <td>11411.670898</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>17287.406250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>15751.861328</td>\n",
       "      <td>14749.724609</td>\n",
       "      <td>12410.792969</td>\n",
       "      <td>14130.139648</td>\n",
       "      <td>NaN</td>\n",
       "      <td>13198.474609</td>\n",
       "      <td>13553.090820</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>IVNS1ABP</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>38411.285156</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10104.601562</td>\n",
       "      <td>18788.167969</td>\n",
       "      <td>10412.311523</td>\n",
       "      <td>17367.800781</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>17287.406250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>15751.861328</td>\n",
       "      <td>14749.724609</td>\n",
       "      <td>12410.792969</td>\n",
       "      <td>14130.139648</td>\n",
       "      <td>7562.620605</td>\n",
       "      <td>13198.474609</td>\n",
       "      <td>13553.090820</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>54863 rows × 36 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                    [1] 20180815_QE3_nLC3_AH_DIA_Honly_ind_01.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                                     NaN            \n",
       "                        MORC2                                                     NaN            \n",
       "                        MORC2                                                     NaN            \n",
       "NS1BP_HUMAN             IVNS1ABP                                                  NaN            \n",
       "                        IVNS1ABP                                                  NaN            \n",
       "\n",
       "                                    [2] 20180815_QE3_nLC3_AH_DIA_Honly_ind_02.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                                     NaN            \n",
       "                        MORC2                                                     NaN            \n",
       "                        MORC2                                                     NaN            \n",
       "NS1BP_HUMAN             IVNS1ABP                                                  NaN            \n",
       "                        IVNS1ABP                                                  NaN            \n",
       "\n",
       "                                    [3] 20180815_QE3_nLC3_AH_DIA_Honly_ind_03.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                             6817.745605            \n",
       "                        MORC2                                             6817.745605            \n",
       "                        MORC2                                             6817.745605            \n",
       "NS1BP_HUMAN             IVNS1ABP                                         38411.285156            \n",
       "                        IVNS1ABP                                         38411.285156            \n",
       "\n",
       "                                    [4] 20180815_QE3_nLC3_AH_DIA_Yonly_ind_01.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                                     NaN            \n",
       "                        MORC2                                                     NaN            \n",
       "                        MORC2                                                     NaN            \n",
       "NS1BP_HUMAN             IVNS1ABP                                                  NaN            \n",
       "                        IVNS1ABP                                                  NaN            \n",
       "\n",
       "                                    [5] 20180815_QE3_nLC3_AH_DIA_Yonly_ind_02.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                                     NaN            \n",
       "                        MORC2                                                     NaN            \n",
       "                        MORC2                                                     NaN            \n",
       "NS1BP_HUMAN             IVNS1ABP                                                  NaN            \n",
       "                        IVNS1ABP                                                  NaN            \n",
       "\n",
       "                                    [6] 20180815_QE3_nLC3_AH_DIA_Yonly_ind_03.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                                     NaN            \n",
       "                        MORC2                                                     NaN            \n",
       "                        MORC2                                                     NaN            \n",
       "NS1BP_HUMAN             IVNS1ABP                                                  NaN            \n",
       "                        IVNS1ABP                                                  NaN            \n",
       "\n",
       "                                    [7] 20180816_QE3_nLC3_AH_DIA_H100_Y100_01.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                       89374.656250            \n",
       "                        TRBV19;TRB                                       89374.656250            \n",
       "                        TRBV19;TRB                                       89374.656250            \n",
       "                        TRBV19;TRB                                       89374.656250            \n",
       "                        TRBV19;TRB                                       89374.656250            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            18010.679688            \n",
       "                        MORC2                                            18010.679688            \n",
       "                        MORC2                                            18010.679688            \n",
       "NS1BP_HUMAN             IVNS1ABP                                         10104.601562            \n",
       "                        IVNS1ABP                                         10104.601562            \n",
       "\n",
       "                                    [8] 20180816_QE3_nLC3_AH_DIA_H100_Y100_02.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "                        TRBV19;TRB                                                NaN            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            12501.521484            \n",
       "                        MORC2                                            12501.521484            \n",
       "                        MORC2                                            12501.521484            \n",
       "NS1BP_HUMAN             IVNS1ABP                                         12773.764648            \n",
       "                        IVNS1ABP                                         18788.167969            \n",
       "\n",
       "                                    [9] 20180816_QE3_nLC3_AH_DIA_H100_Y100_03.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                       90181.578125            \n",
       "                        TRBV19;TRB                                       90181.578125            \n",
       "                        TRBV19;TRB                                       90181.578125            \n",
       "                        TRBV19;TRB                                       90181.578125            \n",
       "                        TRBV19;TRB                                       90181.578125            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            17377.408203            \n",
       "                        MORC2                                            17377.408203            \n",
       "                        MORC2                                            17377.408203            \n",
       "NS1BP_HUMAN             IVNS1ABP                                         10412.311523            \n",
       "                        IVNS1ABP                                         10412.311523            \n",
       "\n",
       "                                    [10] 20180816_QE3_nLC3_AH_DIA_H100_Y100_04.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                     \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                       96197.070312             \n",
       "                        TRBV19;TRB                                       96197.070312             \n",
       "                        TRBV19;TRB                                       96197.070312             \n",
       "                        TRBV19;TRB                                       96197.070312             \n",
       "                        TRBV19;TRB                                       96197.070312             \n",
       "...                                                                               ...             \n",
       "MORC2_HUMAN             MORC2                                            13730.358398             \n",
       "                        MORC2                                            13730.358398             \n",
       "                        MORC2                                            13730.358398             \n",
       "NS1BP_HUMAN             IVNS1ABP                                         11411.670898             \n",
       "                        IVNS1ABP                                         17367.800781             \n",
       "\n",
       "                                    ...  \\\n",
       "proteins                genes       ...   \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB  ...   \n",
       "                        TRBV19;TRB  ...   \n",
       "                        TRBV19;TRB  ...   \n",
       "                        TRBV19;TRB  ...   \n",
       "                        TRBV19;TRB  ...   \n",
       "...                                 ...   \n",
       "MORC2_HUMAN             MORC2       ...   \n",
       "                        MORC2       ...   \n",
       "                        MORC2       ...   \n",
       "NS1BP_HUMAN             IVNS1ABP    ...   \n",
       "                        IVNS1ABP    ...   \n",
       "\n",
       "                                    [27] 20180816_QE3_nLC3_AH_DIA_H100_Y25_03.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                       69968.835938            \n",
       "                        TRBV19;TRB                                       69968.835938            \n",
       "                        TRBV19;TRB                                       69968.835938            \n",
       "                        TRBV19;TRB                                       69968.835938            \n",
       "                        TRBV19;TRB                                       69968.835938            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            23552.466797            \n",
       "                        MORC2                                            23552.466797            \n",
       "                        MORC2                                            23552.466797            \n",
       "NS1BP_HUMAN             IVNS1ABP                                                  NaN            \n",
       "                        IVNS1ABP                                                  NaN            \n",
       "\n",
       "                                    [28] 20180816_QE3_nLC3_AH_DIA_H100_Y25_04.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                      103632.601562            \n",
       "                        TRBV19;TRB                                      103632.601562            \n",
       "                        TRBV19;TRB                                      103632.601562            \n",
       "                        TRBV19;TRB                                      103632.601562            \n",
       "                        TRBV19;TRB                                      103632.601562            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            22144.580078            \n",
       "                        MORC2                                            22144.580078            \n",
       "                        MORC2                                            22144.580078            \n",
       "NS1BP_HUMAN             IVNS1ABP                                         17287.406250            \n",
       "                        IVNS1ABP                                         17287.406250            \n",
       "\n",
       "                                    [29] 20180816_QE3_nLC3_AH_DIA_H100_Y25_05.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                       90488.929688            \n",
       "                        TRBV19;TRB                                       90488.929688            \n",
       "                        TRBV19;TRB                                       90488.929688            \n",
       "                        TRBV19;TRB                                       90488.929688            \n",
       "                        TRBV19;TRB                                       90488.929688            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            20846.851562            \n",
       "                        MORC2                                            20846.851562            \n",
       "                        MORC2                                            20846.851562            \n",
       "NS1BP_HUMAN             IVNS1ABP                                                  NaN            \n",
       "                        IVNS1ABP                                                  NaN            \n",
       "\n",
       "                                    [30] 20180816_QE3_nLC3_AH_DIA_H100_Y25_06.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                      113429.859375            \n",
       "                        TRBV19;TRB                                      113429.859375            \n",
       "                        TRBV19;TRB                                      113429.859375            \n",
       "                        TRBV19;TRB                                      113429.859375            \n",
       "                        TRBV19;TRB                                      113429.859375            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            24248.417969            \n",
       "                        MORC2                                            24248.417969            \n",
       "                        MORC2                                            24248.417969            \n",
       "NS1BP_HUMAN             IVNS1ABP                                         15751.861328            \n",
       "                        IVNS1ABP                                         15751.861328            \n",
       "\n",
       "                                    [31] 20180816_QE3_nLC3_AH_DIA_H100_Y50_01.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                       96970.273438            \n",
       "                        TRBV19;TRB                                       96970.273438            \n",
       "                        TRBV19;TRB                                       96970.273438            \n",
       "                        TRBV19;TRB                                       96970.273438            \n",
       "                        TRBV19;TRB                                       96970.273438            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            22490.054688            \n",
       "                        MORC2                                            22490.054688            \n",
       "                        MORC2                                            22490.054688            \n",
       "NS1BP_HUMAN             IVNS1ABP                                         14749.724609            \n",
       "                        IVNS1ABP                                         14749.724609            \n",
       "\n",
       "                                    [32] 20180816_QE3_nLC3_AH_DIA_H100_Y50_02.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                       61069.171875            \n",
       "                        TRBV19;TRB                                       61069.171875            \n",
       "                        TRBV19;TRB                                       61069.171875            \n",
       "                        TRBV19;TRB                                       61069.171875            \n",
       "                        TRBV19;TRB                                       61069.171875            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            22095.990234            \n",
       "                        MORC2                                            22095.990234            \n",
       "                        MORC2                                            22095.990234            \n",
       "NS1BP_HUMAN             IVNS1ABP                                         12410.792969            \n",
       "                        IVNS1ABP                                         12410.792969            \n",
       "\n",
       "                                    [33] 20180816_QE3_nLC3_AH_DIA_H100_Y50_03.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                       99673.273438            \n",
       "                        TRBV19;TRB                                       99673.273438            \n",
       "                        TRBV19;TRB                                       99673.273438            \n",
       "                        TRBV19;TRB                                       99673.273438            \n",
       "                        TRBV19;TRB                                       99673.273438            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            25553.849609            \n",
       "                        MORC2                                            25553.849609            \n",
       "                        MORC2                                            25553.849609            \n",
       "NS1BP_HUMAN             IVNS1ABP                                         14130.139648            \n",
       "                        IVNS1ABP                                         14130.139648            \n",
       "\n",
       "                                    [34] 20180816_QE3_nLC3_AH_DIA_H100_Y50_04.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                      109199.875000            \n",
       "                        TRBV19;TRB                                      109199.875000            \n",
       "                        TRBV19;TRB                                      109199.875000            \n",
       "                        TRBV19;TRB                                      109199.875000            \n",
       "                        TRBV19;TRB                                      109199.875000            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            22250.546875            \n",
       "                        MORC2                                            22250.546875            \n",
       "                        MORC2                                            22250.546875            \n",
       "NS1BP_HUMAN             IVNS1ABP                                                  NaN            \n",
       "                        IVNS1ABP                                          7562.620605            \n",
       "\n",
       "                                    [35] 20180816_QE3_nLC3_AH_DIA_H100_Y50_05.raw.PTM.Quantity  \\\n",
       "proteins                genes                                                                    \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                      112307.476562            \n",
       "                        TRBV19;TRB                                      112307.476562            \n",
       "                        TRBV19;TRB                                      112307.476562            \n",
       "                        TRBV19;TRB                                      112307.476562            \n",
       "                        TRBV19;TRB                                      112307.476562            \n",
       "...                                                                               ...            \n",
       "MORC2_HUMAN             MORC2                                            14592.869141            \n",
       "                        MORC2                                            14592.869141            \n",
       "                        MORC2                                            14592.869141            \n",
       "NS1BP_HUMAN             IVNS1ABP                                         13198.474609            \n",
       "                        IVNS1ABP                                         13198.474609            \n",
       "\n",
       "                                    [36] 20180816_QE3_nLC3_AH_DIA_H100_Y50_06.raw.PTM.Quantity  \n",
       "proteins                genes                                                                   \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB                                      112374.843750           \n",
       "                        TRBV19;TRB                                      112374.843750           \n",
       "                        TRBV19;TRB                                      112374.843750           \n",
       "                        TRBV19;TRB                                      112374.843750           \n",
       "                        TRBV19;TRB                                      112374.843750           \n",
       "...                                                                               ...           \n",
       "MORC2_HUMAN             MORC2                                            19265.998047           \n",
       "                        MORC2                                            19265.998047           \n",
       "                        MORC2                                            19265.998047           \n",
       "NS1BP_HUMAN             IVNS1ABP                                         13553.090820           \n",
       "                        IVNS1ABP                                         13553.090820           \n",
       "\n",
       "[54863 rows x 36 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Example with custom column mapping\n",
    "reader = pg_reader_provider.get_reader('spectronaut')\n",
    "reader.import_file(spectronaut_example_path)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c3c69b74",
   "metadata": {},
   "source": [
    "Let's say that we are also interested in the PTM site in the sample. We can extract this information as well by using the `add_column_mapping` method:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "e83439c3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>[1] 20180815_QE3_nLC3_AH_DIA_Honly_ind_01.raw.PTM.Quantity</th>\n",
       "      <th>[2] 20180815_QE3_nLC3_AH_DIA_Honly_ind_02.raw.PTM.Quantity</th>\n",
       "      <th>[3] 20180815_QE3_nLC3_AH_DIA_Honly_ind_03.raw.PTM.Quantity</th>\n",
       "      <th>[4] 20180815_QE3_nLC3_AH_DIA_Yonly_ind_01.raw.PTM.Quantity</th>\n",
       "      <th>[5] 20180815_QE3_nLC3_AH_DIA_Yonly_ind_02.raw.PTM.Quantity</th>\n",
       "      <th>[6] 20180815_QE3_nLC3_AH_DIA_Yonly_ind_03.raw.PTM.Quantity</th>\n",
       "      <th>[7] 20180816_QE3_nLC3_AH_DIA_H100_Y100_01.raw.PTM.Quantity</th>\n",
       "      <th>[8] 20180816_QE3_nLC3_AH_DIA_H100_Y100_02.raw.PTM.Quantity</th>\n",
       "      <th>[9] 20180816_QE3_nLC3_AH_DIA_H100_Y100_03.raw.PTM.Quantity</th>\n",
       "      <th>[10] 20180816_QE3_nLC3_AH_DIA_H100_Y100_04.raw.PTM.Quantity</th>\n",
       "      <th>...</th>\n",
       "      <th>[27] 20180816_QE3_nLC3_AH_DIA_H100_Y25_03.raw.PTM.Quantity</th>\n",
       "      <th>[28] 20180816_QE3_nLC3_AH_DIA_H100_Y25_04.raw.PTM.Quantity</th>\n",
       "      <th>[29] 20180816_QE3_nLC3_AH_DIA_H100_Y25_05.raw.PTM.Quantity</th>\n",
       "      <th>[30] 20180816_QE3_nLC3_AH_DIA_H100_Y25_06.raw.PTM.Quantity</th>\n",
       "      <th>[31] 20180816_QE3_nLC3_AH_DIA_H100_Y50_01.raw.PTM.Quantity</th>\n",
       "      <th>[32] 20180816_QE3_nLC3_AH_DIA_H100_Y50_02.raw.PTM.Quantity</th>\n",
       "      <th>[33] 20180816_QE3_nLC3_AH_DIA_H100_Y50_03.raw.PTM.Quantity</th>\n",
       "      <th>[34] 20180816_QE3_nLC3_AH_DIA_H100_Y50_04.raw.PTM.Quantity</th>\n",
       "      <th>[35] 20180816_QE3_nLC3_AH_DIA_H100_Y50_05.raw.PTM.Quantity</th>\n",
       "      <th>[36] 20180816_QE3_nLC3_AH_DIA_H100_Y50_06.raw.PTM.Quantity</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proteins</th>\n",
       "      <th>genes</th>\n",
       "      <th>ptm_site_amino_acid</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th rowspan=\"5\" valign=\"top\">TVB19_HUMAN;TRBR1_HUMAN</th>\n",
       "      <th rowspan=\"5\" valign=\"top\">TRBV19;TRB</th>\n",
       "      <th>S</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>89374.656250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>90181.578125</td>\n",
       "      <td>96197.070312</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.835938</td>\n",
       "      <td>103632.601562</td>\n",
       "      <td>90488.929688</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.273438</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.273438</td>\n",
       "      <td>109199.875000</td>\n",
       "      <td>112307.476562</td>\n",
       "      <td>112374.843750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>S</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>89374.656250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>90181.578125</td>\n",
       "      <td>96197.070312</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.835938</td>\n",
       "      <td>103632.601562</td>\n",
       "      <td>90488.929688</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.273438</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.273438</td>\n",
       "      <td>109199.875000</td>\n",
       "      <td>112307.476562</td>\n",
       "      <td>112374.843750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Y</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>89374.656250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>90181.578125</td>\n",
       "      <td>96197.070312</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.835938</td>\n",
       "      <td>103632.601562</td>\n",
       "      <td>90488.929688</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.273438</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.273438</td>\n",
       "      <td>109199.875000</td>\n",
       "      <td>112307.476562</td>\n",
       "      <td>112374.843750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>S</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>89374.656250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>90181.578125</td>\n",
       "      <td>96197.070312</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.835938</td>\n",
       "      <td>103632.601562</td>\n",
       "      <td>90488.929688</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.273438</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.273438</td>\n",
       "      <td>109199.875000</td>\n",
       "      <td>112307.476562</td>\n",
       "      <td>112374.843750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>S</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>89374.656250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>90181.578125</td>\n",
       "      <td>96197.070312</td>\n",
       "      <td>...</td>\n",
       "      <td>69968.835938</td>\n",
       "      <td>103632.601562</td>\n",
       "      <td>90488.929688</td>\n",
       "      <td>113429.859375</td>\n",
       "      <td>96970.273438</td>\n",
       "      <td>61069.171875</td>\n",
       "      <td>99673.273438</td>\n",
       "      <td>109199.875000</td>\n",
       "      <td>112307.476562</td>\n",
       "      <td>112374.843750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"3\" valign=\"top\">MORC2_HUMAN</th>\n",
       "      <th rowspan=\"3\" valign=\"top\">MORC2</th>\n",
       "      <th>S</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6817.745605</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>18010.679688</td>\n",
       "      <td>12501.521484</td>\n",
       "      <td>17377.408203</td>\n",
       "      <td>13730.358398</td>\n",
       "      <td>...</td>\n",
       "      <td>23552.466797</td>\n",
       "      <td>22144.580078</td>\n",
       "      <td>20846.851562</td>\n",
       "      <td>24248.417969</td>\n",
       "      <td>22490.054688</td>\n",
       "      <td>22095.990234</td>\n",
       "      <td>25553.849609</td>\n",
       "      <td>22250.546875</td>\n",
       "      <td>14592.869141</td>\n",
       "      <td>19265.998047</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>S</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6817.745605</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>18010.679688</td>\n",
       "      <td>12501.521484</td>\n",
       "      <td>17377.408203</td>\n",
       "      <td>13730.358398</td>\n",
       "      <td>...</td>\n",
       "      <td>23552.466797</td>\n",
       "      <td>22144.580078</td>\n",
       "      <td>20846.851562</td>\n",
       "      <td>24248.417969</td>\n",
       "      <td>22490.054688</td>\n",
       "      <td>22095.990234</td>\n",
       "      <td>25553.849609</td>\n",
       "      <td>22250.546875</td>\n",
       "      <td>14592.869141</td>\n",
       "      <td>19265.998047</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>S</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6817.745605</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>18010.679688</td>\n",
       "      <td>12501.521484</td>\n",
       "      <td>17377.408203</td>\n",
       "      <td>13730.358398</td>\n",
       "      <td>...</td>\n",
       "      <td>23552.466797</td>\n",
       "      <td>22144.580078</td>\n",
       "      <td>20846.851562</td>\n",
       "      <td>24248.417969</td>\n",
       "      <td>22490.054688</td>\n",
       "      <td>22095.990234</td>\n",
       "      <td>25553.849609</td>\n",
       "      <td>22250.546875</td>\n",
       "      <td>14592.869141</td>\n",
       "      <td>19265.998047</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"2\" valign=\"top\">NS1BP_HUMAN</th>\n",
       "      <th rowspan=\"2\" valign=\"top\">IVNS1ABP</th>\n",
       "      <th>M</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>38411.285156</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10104.601562</td>\n",
       "      <td>12773.764648</td>\n",
       "      <td>10412.311523</td>\n",
       "      <td>11411.670898</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>17287.406250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>15751.861328</td>\n",
       "      <td>14749.724609</td>\n",
       "      <td>12410.792969</td>\n",
       "      <td>14130.139648</td>\n",
       "      <td>NaN</td>\n",
       "      <td>13198.474609</td>\n",
       "      <td>13553.090820</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>S</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>38411.285156</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10104.601562</td>\n",
       "      <td>18788.167969</td>\n",
       "      <td>10412.311523</td>\n",
       "      <td>17367.800781</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>17287.406250</td>\n",
       "      <td>NaN</td>\n",
       "      <td>15751.861328</td>\n",
       "      <td>14749.724609</td>\n",
       "      <td>12410.792969</td>\n",
       "      <td>14130.139648</td>\n",
       "      <td>7562.620605</td>\n",
       "      <td>13198.474609</td>\n",
       "      <td>13553.090820</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>54863 rows × 36 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                        [1] 20180815_QE3_nLC3_AH_DIA_Honly_ind_01.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   Y                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "\n",
       "                                                        [2] 20180815_QE3_nLC3_AH_DIA_Honly_ind_02.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   Y                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "\n",
       "                                                        [3] 20180815_QE3_nLC3_AH_DIA_Honly_ind_03.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   Y                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                          6817.745605            \n",
       "                                   S                                                          6817.745605            \n",
       "                                   S                                                          6817.745605            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         38411.285156            \n",
       "                                   S                                                         38411.285156            \n",
       "\n",
       "                                                        [4] 20180815_QE3_nLC3_AH_DIA_Yonly_ind_01.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   Y                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "\n",
       "                                                        [5] 20180815_QE3_nLC3_AH_DIA_Yonly_ind_02.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   Y                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "\n",
       "                                                        [6] 20180815_QE3_nLC3_AH_DIA_Yonly_ind_03.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   Y                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "\n",
       "                                                        [7] 20180816_QE3_nLC3_AH_DIA_H100_Y100_01.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                         89374.656250            \n",
       "                                   S                                                         89374.656250            \n",
       "                                   Y                                                         89374.656250            \n",
       "                                   S                                                         89374.656250            \n",
       "                                   S                                                         89374.656250            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         18010.679688            \n",
       "                                   S                                                         18010.679688            \n",
       "                                   S                                                         18010.679688            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         10104.601562            \n",
       "                                   S                                                         10104.601562            \n",
       "\n",
       "                                                        [8] 20180816_QE3_nLC3_AH_DIA_H100_Y100_02.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   Y                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         12501.521484            \n",
       "                                   S                                                         12501.521484            \n",
       "                                   S                                                         12501.521484            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         12773.764648            \n",
       "                                   S                                                         18788.167969            \n",
       "\n",
       "                                                        [9] 20180816_QE3_nLC3_AH_DIA_H100_Y100_03.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                         90181.578125            \n",
       "                                   S                                                         90181.578125            \n",
       "                                   Y                                                         90181.578125            \n",
       "                                   S                                                         90181.578125            \n",
       "                                   S                                                         90181.578125            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         17377.408203            \n",
       "                                   S                                                         17377.408203            \n",
       "                                   S                                                         17377.408203            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         10412.311523            \n",
       "                                   S                                                         10412.311523            \n",
       "\n",
       "                                                        [10] 20180816_QE3_nLC3_AH_DIA_H100_Y100_04.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                                \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                         96197.070312             \n",
       "                                   S                                                         96197.070312             \n",
       "                                   Y                                                         96197.070312             \n",
       "                                   S                                                         96197.070312             \n",
       "                                   S                                                         96197.070312             \n",
       "...                                                                                                   ...             \n",
       "MORC2_HUMAN             MORC2      S                                                         13730.358398             \n",
       "                                   S                                                         13730.358398             \n",
       "                                   S                                                         13730.358398             \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         11411.670898             \n",
       "                                   S                                                         17367.800781             \n",
       "\n",
       "                                                        ...  \\\n",
       "proteins                genes      ptm_site_amino_acid  ...   \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                    ...   \n",
       "                                   S                    ...   \n",
       "                                   Y                    ...   \n",
       "                                   S                    ...   \n",
       "                                   S                    ...   \n",
       "...                                                     ...   \n",
       "MORC2_HUMAN             MORC2      S                    ...   \n",
       "                                   S                    ...   \n",
       "                                   S                    ...   \n",
       "NS1BP_HUMAN             IVNS1ABP   M                    ...   \n",
       "                                   S                    ...   \n",
       "\n",
       "                                                        [27] 20180816_QE3_nLC3_AH_DIA_H100_Y25_03.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                         69968.835938            \n",
       "                                   S                                                         69968.835938            \n",
       "                                   Y                                                         69968.835938            \n",
       "                                   S                                                         69968.835938            \n",
       "                                   S                                                         69968.835938            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         23552.466797            \n",
       "                                   S                                                         23552.466797            \n",
       "                                   S                                                         23552.466797            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "\n",
       "                                                        [28] 20180816_QE3_nLC3_AH_DIA_H100_Y25_04.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                        103632.601562            \n",
       "                                   S                                                        103632.601562            \n",
       "                                   Y                                                        103632.601562            \n",
       "                                   S                                                        103632.601562            \n",
       "                                   S                                                        103632.601562            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         22144.580078            \n",
       "                                   S                                                         22144.580078            \n",
       "                                   S                                                         22144.580078            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         17287.406250            \n",
       "                                   S                                                         17287.406250            \n",
       "\n",
       "                                                        [29] 20180816_QE3_nLC3_AH_DIA_H100_Y25_05.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                         90488.929688            \n",
       "                                   S                                                         90488.929688            \n",
       "                                   Y                                                         90488.929688            \n",
       "                                   S                                                         90488.929688            \n",
       "                                   S                                                         90488.929688            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         20846.851562            \n",
       "                                   S                                                         20846.851562            \n",
       "                                   S                                                         20846.851562            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                                  NaN            \n",
       "                                   S                                                                  NaN            \n",
       "\n",
       "                                                        [30] 20180816_QE3_nLC3_AH_DIA_H100_Y25_06.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                        113429.859375            \n",
       "                                   S                                                        113429.859375            \n",
       "                                   Y                                                        113429.859375            \n",
       "                                   S                                                        113429.859375            \n",
       "                                   S                                                        113429.859375            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         24248.417969            \n",
       "                                   S                                                         24248.417969            \n",
       "                                   S                                                         24248.417969            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         15751.861328            \n",
       "                                   S                                                         15751.861328            \n",
       "\n",
       "                                                        [31] 20180816_QE3_nLC3_AH_DIA_H100_Y50_01.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                         96970.273438            \n",
       "                                   S                                                         96970.273438            \n",
       "                                   Y                                                         96970.273438            \n",
       "                                   S                                                         96970.273438            \n",
       "                                   S                                                         96970.273438            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         22490.054688            \n",
       "                                   S                                                         22490.054688            \n",
       "                                   S                                                         22490.054688            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         14749.724609            \n",
       "                                   S                                                         14749.724609            \n",
       "\n",
       "                                                        [32] 20180816_QE3_nLC3_AH_DIA_H100_Y50_02.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                         61069.171875            \n",
       "                                   S                                                         61069.171875            \n",
       "                                   Y                                                         61069.171875            \n",
       "                                   S                                                         61069.171875            \n",
       "                                   S                                                         61069.171875            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         22095.990234            \n",
       "                                   S                                                         22095.990234            \n",
       "                                   S                                                         22095.990234            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         12410.792969            \n",
       "                                   S                                                         12410.792969            \n",
       "\n",
       "                                                        [33] 20180816_QE3_nLC3_AH_DIA_H100_Y50_03.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                         99673.273438            \n",
       "                                   S                                                         99673.273438            \n",
       "                                   Y                                                         99673.273438            \n",
       "                                   S                                                         99673.273438            \n",
       "                                   S                                                         99673.273438            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         25553.849609            \n",
       "                                   S                                                         25553.849609            \n",
       "                                   S                                                         25553.849609            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         14130.139648            \n",
       "                                   S                                                         14130.139648            \n",
       "\n",
       "                                                        [34] 20180816_QE3_nLC3_AH_DIA_H100_Y50_04.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                        109199.875000            \n",
       "                                   S                                                        109199.875000            \n",
       "                                   Y                                                        109199.875000            \n",
       "                                   S                                                        109199.875000            \n",
       "                                   S                                                        109199.875000            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         22250.546875            \n",
       "                                   S                                                         22250.546875            \n",
       "                                   S                                                         22250.546875            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                                  NaN            \n",
       "                                   S                                                          7562.620605            \n",
       "\n",
       "                                                        [35] 20180816_QE3_nLC3_AH_DIA_H100_Y50_05.raw.PTM.Quantity  \\\n",
       "proteins                genes      ptm_site_amino_acid                                                               \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                        112307.476562            \n",
       "                                   S                                                        112307.476562            \n",
       "                                   Y                                                        112307.476562            \n",
       "                                   S                                                        112307.476562            \n",
       "                                   S                                                        112307.476562            \n",
       "...                                                                                                   ...            \n",
       "MORC2_HUMAN             MORC2      S                                                         14592.869141            \n",
       "                                   S                                                         14592.869141            \n",
       "                                   S                                                         14592.869141            \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         13198.474609            \n",
       "                                   S                                                         13198.474609            \n",
       "\n",
       "                                                        [36] 20180816_QE3_nLC3_AH_DIA_H100_Y50_06.raw.PTM.Quantity  \n",
       "proteins                genes      ptm_site_amino_acid                                                              \n",
       "TVB19_HUMAN;TRBR1_HUMAN TRBV19;TRB S                                                        112374.843750           \n",
       "                                   S                                                        112374.843750           \n",
       "                                   Y                                                        112374.843750           \n",
       "                                   S                                                        112374.843750           \n",
       "                                   S                                                        112374.843750           \n",
       "...                                                                                                   ...           \n",
       "MORC2_HUMAN             MORC2      S                                                         19265.998047           \n",
       "                                   S                                                         19265.998047           \n",
       "                                   S                                                         19265.998047           \n",
       "NS1BP_HUMAN             IVNS1ABP   M                                                         13553.090820           \n",
       "                                   S                                                         13553.090820           \n",
       "\n",
       "[54863 rows x 36 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Add custom column mapping for organism information\n",
    "reader.add_column_mapping({\"ptm_site_amino_acid\": \"PTM.SiteAA\"})\n",
    "reader.import_file(spectronaut_example_path)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ba18279a",
   "metadata": {},
   "source": [
    "## scVerse compatibility \n",
    "\n",
    "The standardized format also allows users to easily convert the protein group tables to widely used `-omics` formats like `anndata.AnnData`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "6cee0251",
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_anndata_from_pg_matrix(file_path: str, search_engine: str, **kwargs) -> ad.AnnData:\n",
    "    \"\"\"Get anndata object from PG matrix.\"\"\"\n",
    "\n",
    "    reader = pg_reader_provider.get_reader(search_engine, **kwargs)\n",
    "    df = reader.import_file(file_path)\n",
    "    return ad.AnnData(\n",
    "        X=df.values.T,\n",
    "        var=df.index.to_frame(),\n",
    "        obs = df.columns.to_frame(name=\"sample_id\")\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "6619e5f6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 6 × 9364\n",
       "    obs: 'sample_id'\n",
       "    var: 'uniprot_ids'"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata = create_anndata_from_pg_matrix(\n",
    "    alphadia_example_path, search_engine=\"alphadia\"\n",
    ")\n",
    "\n",
    "adata"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ce2e70a6",
   "metadata": {},
   "source": [
    "## Conclusion\n",
    "\n",
    "The alphabase protein group reader module provides:\n",
    "\n",
    "- **Unified interface** for reading protein group tables from multiple search engines\n",
    "- **Standardized output format** that facilitates cross-engine comparisons and downstream analyses\n",
    "- **Flexible quantification options** to extract different measurement types (raw, LFQ, iBAQ)\n",
    "- **Extensible architecture** that supports custom column mappings and new search engines\n",
    "\n",
    "This standardization enables researchers to focus on biological insights rather than data format complexities."
   ]
  }
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