sandbox/05_dda_library.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Example Notebook\n",
    "\n",
    "Building a spectral library for DIA-NN based on AlphaPept search results with AlphaPeptDeep"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Installation & File Download\n",
    "\n",
    "Follow the installation instructions for [AlphaPeptDeep](https://github.com/MannLabs/alphapeptdeep), i.e.:\n",
    "\n",
    "!pip install alphabase peptdeep"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.0.2\n"
     ]
    }
   ],
   "source": [
    "import peptdeep\n",
    "\n",
    "print(peptdeep.__version__)   "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Download the files\n",
    "\n",
    "import os\n",
    "try:\n",
    "    import wget\n",
    "except ModuleNotFoundError:\n",
    "    !pip install wget\n",
    "    import wget\n",
    "    \n",
    "FILE_DICT = {}\n",
    "FILE_DICT['thermo_IRT.ms_data.hdf'] = 'https://datashare.biochem.mpg.de/s/oUkKeB0SraHATrh/download'\n",
    "\n",
    "tmp_folder = os.path.join(os.getcwd(),'/temp_test_run')\n",
    "\n",
    "if not os.path.isdir(tmp_folder):\n",
    "    os.mkdir(tmp_folder)\n",
    "    \n",
    "for file in FILE_DICT:\n",
    "    target = os.path.join(tmp_folder, file)\n",
    "    if not os.path.isfile(target):\n",
    "        wget.download(FILE_DICT[file], target)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load DataFrame and import to AlphaPeptDeep"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "ap_ms_data_hdf = os.path.join(tmp_folder,'thermo_IRT.ms_data.hdf')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "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>rt</th>\n",
       "      <th>scan_num</th>\n",
       "      <th>spec_idx</th>\n",
       "      <th>query_id</th>\n",
       "      <th>score</th>\n",
       "      <th>precursor_mz</th>\n",
       "      <th>charge</th>\n",
       "      <th>raw_name</th>\n",
       "      <th>fdr</th>\n",
       "      <th>decoy</th>\n",
       "      <th>sequence</th>\n",
       "      <th>mods</th>\n",
       "      <th>mod_sites</th>\n",
       "      <th>nAA</th>\n",
       "      <th>rt_norm</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2.050556</td>\n",
       "      <td>937</td>\n",
       "      <td>936</td>\n",
       "      <td>1536</td>\n",
       "      <td>0.765814</td>\n",
       "      <td>508.262939</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>LGGNEQVTR</td>\n",
       "      <td>Acetyl@Protein N-term</td>\n",
       "      <td>0</td>\n",
       "      <td>9</td>\n",
       "      <td>0.352973</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2.050556</td>\n",
       "      <td>927</td>\n",
       "      <td>926</td>\n",
       "      <td>1535</td>\n",
       "      <td>0.744933</td>\n",
       "      <td>508.262939</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>LGGNEQVTR</td>\n",
       "      <td>Acetyl@Protein N-term</td>\n",
       "      <td>0</td>\n",
       "      <td>9</td>\n",
       "      <td>0.352973</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>4.792137</td>\n",
       "      <td>3337</td>\n",
       "      <td>3336</td>\n",
       "      <td>2242</td>\n",
       "      <td>0.846333</td>\n",
       "      <td>683.857632</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>TPVITGAPYEYR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>0.824895</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4.792137</td>\n",
       "      <td>3399</td>\n",
       "      <td>3398</td>\n",
       "      <td>2241</td>\n",
       "      <td>0.836358</td>\n",
       "      <td>683.857632</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>TPVITGAPYEYR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>0.824895</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>2.794513</td>\n",
       "      <td>1732</td>\n",
       "      <td>1731</td>\n",
       "      <td>2237</td>\n",
       "      <td>0.786324</td>\n",
       "      <td>456.238705</td>\n",
       "      <td>3</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>TPVITGAPYEYR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>0.481034</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>2.508832</td>\n",
       "      <td>1409</td>\n",
       "      <td>1408</td>\n",
       "      <td>2239</td>\n",
       "      <td>0.744924</td>\n",
       "      <td>456.239318</td>\n",
       "      <td>3</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>TPVITGAPYEYR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>0.431858</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>2.219010</td>\n",
       "      <td>1150</td>\n",
       "      <td>1149</td>\n",
       "      <td>2236</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>683.828846</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>VEATFGVDESNAK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>0.381969</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>3.189371</td>\n",
       "      <td>2102</td>\n",
       "      <td>2101</td>\n",
       "      <td>2373</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>466.561822</td>\n",
       "      <td>3</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>DGLDAASYYAPVR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>0.549003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>5.804992</td>\n",
       "      <td>3827</td>\n",
       "      <td>3826</td>\n",
       "      <td>2235</td>\n",
       "      <td>0.756397</td>\n",
       "      <td>683.828439</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>VEATFGVDESNAK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>0.999243</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>5.809390</td>\n",
       "      <td>3833</td>\n",
       "      <td>3832</td>\n",
       "      <td>2377</td>\n",
       "      <td>0.747592</td>\n",
       "      <td>699.339856</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>DGLDAASYYAPVR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>1.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>3.187733</td>\n",
       "      <td>2308</td>\n",
       "      <td>2307</td>\n",
       "      <td>2016</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>644.823877</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>GAGSSEPVTGLDAK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "      <td>0.548721</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>4.967367</td>\n",
       "      <td>3306</td>\n",
       "      <td>3305</td>\n",
       "      <td>2018</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>644.825372</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>GAGSSEPVTGLDAK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "      <td>0.855058</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>4.927158</td>\n",
       "      <td>3272</td>\n",
       "      <td>3271</td>\n",
       "      <td>2825</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>776.932954</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>LFLQFGAQGSPFLK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "      <td>0.848137</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>4.970473</td>\n",
       "      <td>3343</td>\n",
       "      <td>3342</td>\n",
       "      <td>2824</td>\n",
       "      <td>0.781208</td>\n",
       "      <td>518.289838</td>\n",
       "      <td>3</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>LFLQFGAQGSPFLK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "      <td>0.855593</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          rt  scan_num  spec_idx  query_id     score  precursor_mz  charge  \\\n",
       "0   2.050556       937       936      1536  0.765814    508.262939       2   \n",
       "1   2.050556       927       926      1535  0.744933    508.262939       2   \n",
       "2   4.792137      3337      3336      2242  0.846333    683.857632       2   \n",
       "3   4.792137      3399      3398      2241  0.836358    683.857632       2   \n",
       "4   2.794513      1732      1731      2237  0.786324    456.238705       3   \n",
       "5   2.508832      1409      1408      2239  0.744924    456.239318       3   \n",
       "6   2.219010      1150      1149      2236  1.000000    683.828846       2   \n",
       "7   3.189371      2102      2101      2373  1.000000    466.561822       3   \n",
       "8   5.804992      3827      3826      2235  0.756397    683.828439       2   \n",
       "9   5.809390      3833      3832      2377  0.747592    699.339856       2   \n",
       "10  3.187733      2308      2307      2016  1.000000    644.823877       2   \n",
       "11  4.967367      3306      3305      2018  1.000000    644.825372       2   \n",
       "12  4.927158      3272      3271      2825  1.000000    776.932954       2   \n",
       "13  4.970473      3343      3342      2824  0.781208    518.289838       3   \n",
       "\n",
       "      raw_name  fdr  decoy        sequence                   mods mod_sites  \\\n",
       "0   thermo_IRT  0.0      0       LGGNEQVTR  Acetyl@Protein N-term         0   \n",
       "1   thermo_IRT  0.0      0       LGGNEQVTR  Acetyl@Protein N-term         0   \n",
       "2   thermo_IRT  0.0      0    TPVITGAPYEYR                                    \n",
       "3   thermo_IRT  0.0      0    TPVITGAPYEYR                                    \n",
       "4   thermo_IRT  0.0      0    TPVITGAPYEYR                                    \n",
       "5   thermo_IRT  0.0      0    TPVITGAPYEYR                                    \n",
       "6   thermo_IRT  0.0      0   VEATFGVDESNAK                                    \n",
       "7   thermo_IRT  0.0      0   DGLDAASYYAPVR                                    \n",
       "8   thermo_IRT  0.0      0   VEATFGVDESNAK                                    \n",
       "9   thermo_IRT  0.0      0   DGLDAASYYAPVR                                    \n",
       "10  thermo_IRT  0.0      0  GAGSSEPVTGLDAK                                    \n",
       "11  thermo_IRT  0.0      0  GAGSSEPVTGLDAK                                    \n",
       "12  thermo_IRT  0.0      0  LFLQFGAQGSPFLK                                    \n",
       "13  thermo_IRT  0.0      0  LFLQFGAQGSPFLK                                    \n",
       "\n",
       "    nAA   rt_norm  \n",
       "0     9  0.352973  \n",
       "1     9  0.352973  \n",
       "2    12  0.824895  \n",
       "3    12  0.824895  \n",
       "4    12  0.481034  \n",
       "5    12  0.431858  \n",
       "6    13  0.381969  \n",
       "7    13  0.549003  \n",
       "8    13  0.999243  \n",
       "9    13  1.000000  \n",
       "10   14  0.548721  \n",
       "11   14  0.855058  \n",
       "12   14  0.848137  \n",
       "13   14  0.855593  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from alphabase.io.psm_reader.alphapept_reader import AlphaPeptReader\n",
    "\n",
    "modification_mapping = {\n",
    "    'Carbamidomethyl@C': 'cC',\n",
    "    'Oxidation@M': 'oxM',\n",
    "    'Phospho@S': 'pS',\n",
    "    'Phospho@T': 'pT',\n",
    "    'Phospho@Y': 'pY',\n",
    "    'Acetyl@Protein N-term': 'a',\n",
    "}\n",
    "\n",
    "reader = AlphaPeptReader(modification_mapping=modification_mapping)\n",
    "reader.import_file(ap_ms_data_hdf)\n",
    "reader.psm_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Extract fragment intensities from the spectrum file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>rt</th>\n",
       "      <th>scan_num</th>\n",
       "      <th>spec_idx</th>\n",
       "      <th>query_id</th>\n",
       "      <th>score</th>\n",
       "      <th>precursor_mz</th>\n",
       "      <th>charge</th>\n",
       "      <th>raw_name</th>\n",
       "      <th>fdr</th>\n",
       "      <th>decoy</th>\n",
       "      <th>sequence</th>\n",
       "      <th>mods</th>\n",
       "      <th>mod_sites</th>\n",
       "      <th>nAA</th>\n",
       "      <th>rt_norm</th>\n",
       "      <th>frag_start_idx</th>\n",
       "      <th>frag_stop_idx</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2.050556</td>\n",
       "      <td>937</td>\n",
       "      <td>936</td>\n",
       "      <td>1536</td>\n",
       "      <td>0.765814</td>\n",
       "      <td>508.262939</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>LGGNEQVTR</td>\n",
       "      <td>Acetyl@Protein N-term</td>\n",
       "      <td>0</td>\n",
       "      <td>9</td>\n",
       "      <td>0.352973</td>\n",
       "      <td>0</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2.050556</td>\n",
       "      <td>927</td>\n",
       "      <td>926</td>\n",
       "      <td>1535</td>\n",
       "      <td>0.744933</td>\n",
       "      <td>508.262939</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>LGGNEQVTR</td>\n",
       "      <td>Acetyl@Protein N-term</td>\n",
       "      <td>0</td>\n",
       "      <td>9</td>\n",
       "      <td>0.352973</td>\n",
       "      <td>8</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>4.792137</td>\n",
       "      <td>3337</td>\n",
       "      <td>3336</td>\n",
       "      <td>2242</td>\n",
       "      <td>0.846333</td>\n",
       "      <td>683.857632</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>TPVITGAPYEYR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>0.824895</td>\n",
       "      <td>16</td>\n",
       "      <td>27</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4.792137</td>\n",
       "      <td>3399</td>\n",
       "      <td>3398</td>\n",
       "      <td>2241</td>\n",
       "      <td>0.836358</td>\n",
       "      <td>683.857632</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>TPVITGAPYEYR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>0.824895</td>\n",
       "      <td>27</td>\n",
       "      <td>38</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>2.794513</td>\n",
       "      <td>1732</td>\n",
       "      <td>1731</td>\n",
       "      <td>2237</td>\n",
       "      <td>0.786324</td>\n",
       "      <td>456.238705</td>\n",
       "      <td>3</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>TPVITGAPYEYR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>0.481034</td>\n",
       "      <td>38</td>\n",
       "      <td>49</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>2.508832</td>\n",
       "      <td>1409</td>\n",
       "      <td>1408</td>\n",
       "      <td>2239</td>\n",
       "      <td>0.744924</td>\n",
       "      <td>456.239318</td>\n",
       "      <td>3</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>TPVITGAPYEYR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>0.431858</td>\n",
       "      <td>49</td>\n",
       "      <td>60</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>2.219010</td>\n",
       "      <td>1150</td>\n",
       "      <td>1149</td>\n",
       "      <td>2236</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>683.828846</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>VEATFGVDESNAK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>0.381969</td>\n",
       "      <td>60</td>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>3.189371</td>\n",
       "      <td>2102</td>\n",
       "      <td>2101</td>\n",
       "      <td>2373</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>466.561822</td>\n",
       "      <td>3</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>DGLDAASYYAPVR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>0.549003</td>\n",
       "      <td>72</td>\n",
       "      <td>84</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>5.804992</td>\n",
       "      <td>3827</td>\n",
       "      <td>3826</td>\n",
       "      <td>2235</td>\n",
       "      <td>0.756397</td>\n",
       "      <td>683.828439</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>VEATFGVDESNAK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>0.999243</td>\n",
       "      <td>84</td>\n",
       "      <td>96</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>5.809390</td>\n",
       "      <td>3833</td>\n",
       "      <td>3832</td>\n",
       "      <td>2377</td>\n",
       "      <td>0.747592</td>\n",
       "      <td>699.339856</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>DGLDAASYYAPVR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>96</td>\n",
       "      <td>108</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>3.187733</td>\n",
       "      <td>2308</td>\n",
       "      <td>2307</td>\n",
       "      <td>2016</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>644.823877</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>GAGSSEPVTGLDAK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "      <td>0.548721</td>\n",
       "      <td>108</td>\n",
       "      <td>121</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>4.967367</td>\n",
       "      <td>3306</td>\n",
       "      <td>3305</td>\n",
       "      <td>2018</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>644.825372</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>GAGSSEPVTGLDAK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "      <td>0.855058</td>\n",
       "      <td>121</td>\n",
       "      <td>134</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>4.927158</td>\n",
       "      <td>3272</td>\n",
       "      <td>3271</td>\n",
       "      <td>2825</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>776.932954</td>\n",
       "      <td>2</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>LFLQFGAQGSPFLK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "      <td>0.848137</td>\n",
       "      <td>134</td>\n",
       "      <td>147</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>4.970473</td>\n",
       "      <td>3343</td>\n",
       "      <td>3342</td>\n",
       "      <td>2824</td>\n",
       "      <td>0.781208</td>\n",
       "      <td>518.289838</td>\n",
       "      <td>3</td>\n",
       "      <td>thermo_IRT</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>LFLQFGAQGSPFLK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "      <td>0.855593</td>\n",
       "      <td>147</td>\n",
       "      <td>160</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          rt  scan_num  spec_idx  query_id     score  precursor_mz  charge  \\\n",
       "0   2.050556       937       936      1536  0.765814    508.262939       2   \n",
       "1   2.050556       927       926      1535  0.744933    508.262939       2   \n",
       "2   4.792137      3337      3336      2242  0.846333    683.857632       2   \n",
       "3   4.792137      3399      3398      2241  0.836358    683.857632       2   \n",
       "4   2.794513      1732      1731      2237  0.786324    456.238705       3   \n",
       "5   2.508832      1409      1408      2239  0.744924    456.239318       3   \n",
       "6   2.219010      1150      1149      2236  1.000000    683.828846       2   \n",
       "7   3.189371      2102      2101      2373  1.000000    466.561822       3   \n",
       "8   5.804992      3827      3826      2235  0.756397    683.828439       2   \n",
       "9   5.809390      3833      3832      2377  0.747592    699.339856       2   \n",
       "10  3.187733      2308      2307      2016  1.000000    644.823877       2   \n",
       "11  4.967367      3306      3305      2018  1.000000    644.825372       2   \n",
       "12  4.927158      3272      3271      2825  1.000000    776.932954       2   \n",
       "13  4.970473      3343      3342      2824  0.781208    518.289838       3   \n",
       "\n",
       "      raw_name  fdr  decoy        sequence                   mods mod_sites  \\\n",
       "0   thermo_IRT  0.0      0       LGGNEQVTR  Acetyl@Protein N-term         0   \n",
       "1   thermo_IRT  0.0      0       LGGNEQVTR  Acetyl@Protein N-term         0   \n",
       "2   thermo_IRT  0.0      0    TPVITGAPYEYR                                    \n",
       "3   thermo_IRT  0.0      0    TPVITGAPYEYR                                    \n",
       "4   thermo_IRT  0.0      0    TPVITGAPYEYR                                    \n",
       "5   thermo_IRT  0.0      0    TPVITGAPYEYR                                    \n",
       "6   thermo_IRT  0.0      0   VEATFGVDESNAK                                    \n",
       "7   thermo_IRT  0.0      0   DGLDAASYYAPVR                                    \n",
       "8   thermo_IRT  0.0      0   VEATFGVDESNAK                                    \n",
       "9   thermo_IRT  0.0      0   DGLDAASYYAPVR                                    \n",
       "10  thermo_IRT  0.0      0  GAGSSEPVTGLDAK                                    \n",
       "11  thermo_IRT  0.0      0  GAGSSEPVTGLDAK                                    \n",
       "12  thermo_IRT  0.0      0  LFLQFGAQGSPFLK                                    \n",
       "13  thermo_IRT  0.0      0  LFLQFGAQGSPFLK                                    \n",
       "\n",
       "    nAA   rt_norm  frag_start_idx  frag_stop_idx  \n",
       "0     9  0.352973               0              8  \n",
       "1     9  0.352973               8             16  \n",
       "2    12  0.824895              16             27  \n",
       "3    12  0.824895              27             38  \n",
       "4    12  0.481034              38             49  \n",
       "5    12  0.431858              49             60  \n",
       "6    13  0.381969              60             72  \n",
       "7    13  0.549003              72             84  \n",
       "8    13  0.999243              84             96  \n",
       "9    13  1.000000              96            108  \n",
       "10   14  0.548721             108            121  \n",
       "11   14  0.855058             121            134  \n",
       "12   14  0.848137             134            147  \n",
       "13   14  0.855593             147            160  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from peptdeep.rescore.feature_extractor import match_one_raw\n",
    "\n",
    "psm_df, frag_mz_df, frag_intensity_df, frag_merr_df = match_one_raw(\n",
    "    reader.psm_df, ms2_file=ap_ms_data_hdf,\n",
    "    ms2_file_type='alphapept',\n",
    "    frag_types_to_match=['b_z1','b_z2','y_z1','y_z2'],\n",
    "    ms2_ppm=True, ms2_tol=50.0,\n",
    "    calibrate_frag_mass_error=False,\n",
    ")\n",
    "psm_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Generate the library for DiaNN"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "from peptdeep.protein.fasta import SpecLibFasta\n",
    "\n",
    "fasta_lib = SpecLibFasta()\n",
    "\n",
    "fasta_lib._precursor_df = psm_df\n",
    "fasta_lib._fragment_mz_df = frag_mz_df\n",
    "fasta_lib._fragment_intensity_df = frag_intensity_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:01<00:00,  1.57s/it]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Translation finished, it will take several minutes to export the rest precursors to the tsv file...\n"
     ]
    }
   ],
   "source": [
    "from peptdeep.spec_lib.translate import translate_to_tsv\n",
    "translate_to_tsv(\n",
    "    fasta_lib, \n",
    "    tsv = ap_ms_data_hdf[:-len('ms_data.hdf')]+'tsv',\n",
    "    min_frag_intensity=0.001,\n",
    "    keep_k_highest_fragments=1000, #keep all matched fragments\n",
    ")"
   ]
  }
 ],
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