diff --git a/alphabase/spectral_library/base.py b/alphabase/spectral_library/base.py
index 671b333f..5361bd45 100644
--- a/alphabase/spectral_library/base.py
+++ b/alphabase/spectral_library/base.py
@@ -193,6 +193,7 @@ def append(
         other: "SpecLibBase",
         dfs_to_append: typing.List[str] = [
             "_precursor_df",
+            "_fragment_df",
             "_fragment_intensity_df",
             "_fragment_mz_df",
             "_fragment_intensity_predicted_df",
@@ -224,6 +225,7 @@ def append(
         None
 
         """
+
         if remove_unused_dfs:
             current_frag_dfs = self.available_dense_fragment_dfs()
             for attr in current_frag_dfs:
@@ -263,15 +265,16 @@ def check_matching_columns(df1, df2):
             else:
                 matching_columns.append([])
 
-        n_fragments = []
+        n_dense_fragments = []
+
         # get subset of dfs_to_append starting with _fragment
         for attr in dfs_to_append:
-            if attr.startswith("_fragment") and hasattr(self, attr):
+            if attr in self.available_dense_fragment_dfs() and hasattr(self, attr):
                 n_current_fragments = len(getattr(self, attr))
                 if n_current_fragments > 0:
-                    n_fragments += [n_current_fragments]
+                    n_dense_fragments += [n_current_fragments]
 
-        if not np.all(np.array(n_fragments) == n_fragments[0]):
+        if len(set(n_dense_fragments)) > 1:
             raise ValueError(
                 "The libraries can't be appended as the number of fragments in the current libraries are not the same."
             )
@@ -284,19 +287,44 @@ def check_matching_columns(df1, df2):
                 other_df = getattr(other, attr)[column].copy()
 
                 if attr.startswith("_precursor"):
-                    frag_idx_increment = 0
-                    for fragment_df in ["_fragment_intensity_df", "_fragment_mz_df"]:
-                        if (
-                            hasattr(self, fragment_df)
-                            and len(getattr(self, fragment_df)) > 0
-                        ):
-                            frag_idx_increment = len(getattr(self, fragment_df))
-
-                    if "frag_start_idx" in other_df.columns:
-                        other_df["frag_start_idx"] += frag_idx_increment
-
-                    if "frag_stop_idx" in other_df.columns:
-                        other_df["frag_stop_idx"] += frag_idx_increment
+                    # we iterate over the types of fragment dataframes
+                    fragment_df_mapping = {
+                        # dense fragment dataframes
+                        "": ["_fragment_intensity_df", "_fragment_mz_df"],
+                        # flat fragment dataframes
+                        "flat_": ["_fragment_df"],
+                    }
+
+                    # Update indices for each fragment dataframe type
+                    for prefix, fragment_df_list in fragment_df_mapping.items():
+                        # obtain frag_idx_increment and check if it is the same for all fragment dataframes
+                        # an increment of 0 is allowed, but if not 0, it must be the same for all dense fragment dataframes
+                        frag_idx_increment = 0
+                        for fragment_df in fragment_df_list:
+                            if (
+                                hasattr(self, fragment_df)
+                                and len(getattr(self, fragment_df)) > 0
+                            ):
+                                if (
+                                    frag_idx_increment != 0
+                                    and len(getattr(self, fragment_df)) != 0
+                                    and frag_idx_increment
+                                    != len(getattr(self, fragment_df))
+                                ):
+                                    raise ValueError(
+                                        f"The number of fragments in the {fragment_df} dataframe must be the same as in all other dense fragment dataframes"
+                                    )
+                                else:
+                                    frag_idx_increment = len(getattr(self, fragment_df))
+
+                        # update the indices
+                        start_col = f"{prefix}frag_start_idx"
+                        stop_col = f"{prefix}frag_stop_idx"
+
+                        if start_col in other_df.columns:
+                            other_df[start_col] += frag_idx_increment
+                        if stop_col in other_df.columns:
+                            other_df[stop_col] += frag_idx_increment
 
                 setattr(
                     self,
diff --git a/alphabase/spectral_library/flat.py b/alphabase/spectral_library/flat.py
index 62e9db7c..e1944c05 100644
--- a/alphabase/spectral_library/flat.py
+++ b/alphabase/spectral_library/flat.py
@@ -81,12 +81,6 @@ def protein_df(self) -> pd.DataFrame:
         """Protein dataframe"""
         return self._protein_df
 
-    def available_dense_fragment_dfs(self):
-        """Return the available dense fragment dataframes.
-        This method is inherited from :class:`SpecLibBase` and will return an empty list for a flat library.
-        """
-        return []
-
     def remove_unused_fragments(self):
         """Remove unused fragments from fragment_df.
         This method is inherited from :class:`SpecLibBase` and has not been implemented for a flat library.
diff --git a/nbs_tests/spectral_library/flat_library.ipynb b/nbs_tests/spectral_library/flat_library.ipynb
index d371863e..6f80b275 100644
--- a/nbs_tests/spectral_library/flat_library.ipynb
+++ b/nbs_tests/spectral_library/flat_library.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -11,24 +11,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from alphabase.spectral_library.flat import *"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,341 +33,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "100%|██████████| 6/6 [00:00<00:00, 2663.05it/s]\n"
-     ]
-    },
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        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>mz</th>\n",
-       "      <th>intensity</th>\n",
-       "      <th>type</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>609.300781</td>\n",
-       "      <td>0.450362</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1</th>\n",
-       "      <td>511.323853</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>2</th>\n",
-       "      <td>510.232330</td>\n",
-       "      <td>0.106543</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>3</th>\n",
-       "      <td>412.255432</td>\n",
-       "      <td>0.374123</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4</th>\n",
-       "      <td>411.163940</td>\n",
-       "      <td>0.069116</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>5</th>\n",
-       "      <td>313.187042</td>\n",
-       "      <td>0.173858</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>6</th>\n",
-       "      <td>321.694702</td>\n",
-       "      <td>0.515072</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>7</th>\n",
-       "      <td>545.329346</td>\n",
-       "      <td>0.745664</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>8</th>\n",
-       "      <td>326.171051</td>\n",
-       "      <td>0.143703</td>\n",
-       "      <td>98</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>9</th>\n",
-       "      <td>432.245270</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>10</th>\n",
-       "      <td>397.208160</td>\n",
-       "      <td>0.094888</td>\n",
-       "      <td>98</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>11</th>\n",
-       "      <td>361.208160</td>\n",
-       "      <td>0.377585</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>12</th>\n",
-       "      <td>496.276581</td>\n",
-       "      <td>0.054980</td>\n",
-       "      <td>98</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>13</th>\n",
-       "      <td>686.275635</td>\n",
-       "      <td>0.103734</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>14</th>\n",
-       "      <td>588.298767</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>15</th>\n",
-       "      <td>349.171783</td>\n",
-       "      <td>0.092058</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>16</th>\n",
-       "      <td>661.295654</td>\n",
-       "      <td>0.198974</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>17</th>\n",
-       "      <td>563.318787</td>\n",
-       "      <td>0.774316</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>18</th>\n",
-       "      <td>494.297302</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>19</th>\n",
-       "      <td>256.129181</td>\n",
-       "      <td>0.649715</td>\n",
-       "      <td>98</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>20</th>\n",
-       "      <td>347.228882</td>\n",
-       "      <td>0.882733</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>21</th>\n",
-       "      <td>403.197601</td>\n",
-       "      <td>0.351781</td>\n",
-       "      <td>98</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>22</th>\n",
-       "      <td>490.229614</td>\n",
-       "      <td>0.400474</td>\n",
-       "      <td>98</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>23</th>\n",
-       "      <td>701.290588</td>\n",
-       "      <td>0.244350</td>\n",
-       "      <td>98</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>24</th>\n",
-       "      <td>603.313660</td>\n",
-       "      <td>0.631000</td>\n",
-       "      <td>98</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>25</th>\n",
-       "      <td>762.258301</td>\n",
-       "      <td>0.084908</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>26</th>\n",
-       "      <td>664.281433</td>\n",
-       "      <td>0.328738</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>27</th>\n",
-       "      <td>497.283051</td>\n",
-       "      <td>0.284129</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>28</th>\n",
-       "      <td>496.191528</td>\n",
-       "      <td>0.276969</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>29</th>\n",
-       "      <td>268.165558</td>\n",
-       "      <td>0.057554</td>\n",
-       "      <td>98</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>30</th>\n",
-       "      <td>398.214630</td>\n",
-       "      <td>0.262853</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>31</th>\n",
-       "      <td>267.074036</td>\n",
-       "      <td>0.087439</td>\n",
-       "      <td>98</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>32</th>\n",
-       "      <td>329.193176</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>33</th>\n",
-       "      <td>435.163940</td>\n",
-       "      <td>0.061627</td>\n",
-       "      <td>98</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>34</th>\n",
-       "      <td>698.312073</td>\n",
-       "      <td>0.602346</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>35</th>\n",
-       "      <td>600.335144</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>36</th>\n",
-       "      <td>611.280029</td>\n",
-       "      <td>0.141106</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>37</th>\n",
-       "      <td>513.303101</td>\n",
-       "      <td>0.705295</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>38</th>\n",
-       "      <td>498.195953</td>\n",
-       "      <td>0.108914</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>39</th>\n",
-       "      <td>400.219055</td>\n",
-       "      <td>0.279959</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>40</th>\n",
-       "      <td>331.197601</td>\n",
-       "      <td>0.492018</td>\n",
-       "      <td>121</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "            mz  intensity  type\n",
-       "0   609.300781   0.450362   121\n",
-       "1   511.323853   1.000000   121\n",
-       "2   510.232330   0.106543   121\n",
-       "3   412.255432   0.374123   121\n",
-       "4   411.163940   0.069116   121\n",
-       "5   313.187042   0.173858   121\n",
-       "6   321.694702   0.515072   121\n",
-       "7   545.329346   0.745664   121\n",
-       "8   326.171051   0.143703    98\n",
-       "9   432.245270   1.000000   121\n",
-       "10  397.208160   0.094888    98\n",
-       "11  361.208160   0.377585   121\n",
-       "12  496.276581   0.054980    98\n",
-       "13  686.275635   0.103734   121\n",
-       "14  588.298767   1.000000   121\n",
-       "15  349.171783   0.092058   121\n",
-       "16  661.295654   0.198974   121\n",
-       "17  563.318787   0.774316   121\n",
-       "18  494.297302   1.000000   121\n",
-       "19  256.129181   0.649715    98\n",
-       "20  347.228882   0.882733   121\n",
-       "21  403.197601   0.351781    98\n",
-       "22  490.229614   0.400474    98\n",
-       "23  701.290588   0.244350    98\n",
-       "24  603.313660   0.631000    98\n",
-       "25  762.258301   0.084908   121\n",
-       "26  664.281433   0.328738   121\n",
-       "27  497.283051   0.284129   121\n",
-       "28  496.191528   0.276969   121\n",
-       "29  268.165558   0.057554    98\n",
-       "30  398.214630   0.262853   121\n",
-       "31  267.074036   0.087439    98\n",
-       "32  329.193176   1.000000   121\n",
-       "33  435.163940   0.061627    98\n",
-       "34  698.312073   0.602346   121\n",
-       "35  600.335144   1.000000   121\n",
-       "36  611.280029   0.141106   121\n",
-       "37  513.303101   0.705295   121\n",
-       "38  498.195953   0.108914   121\n",
-       "39  400.219055   0.279959   121\n",
-       "40  331.197601   0.492018   121"
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "#| hide\n",
     "tsv_str = \"\"\"PrecursorCharge\tModifiedPeptide\tStrippedPeptide\tiRT\tLabeledPeptide\tPrecursorMz\tFragmentLossType\tFragmentNumber\tFragmentType\tFragmentCharge\tFragmentMz\tRelativeIntensity\tIonMobility\n",
@@ -439,182 +97,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        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>nAA</th>\n",
-       "      <th>sequence</th>\n",
-       "      <th>charge</th>\n",
-       "      <th>mobility</th>\n",
-       "      <th>precursor_mz</th>\n",
-       "      <th>rt</th>\n",
-       "      <th>mods</th>\n",
-       "      <th>mod_sites</th>\n",
-       "      <th>frag_start_idx</th>\n",
-       "      <th>frag_stop_idx</th>\n",
-       "      <th>rt_norm</th>\n",
-       "      <th>ccs</th>\n",
-       "      <th>flat_frag_start_idx</th>\n",
-       "      <th>flat_frag_stop_idx</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>7</td>\n",
-       "      <td>AVVVSPK</td>\n",
-       "      <td>2</td>\n",
-       "      <td>0.9</td>\n",
-       "      <td>390.206779</td>\n",
-       "      <td>-22.849740</td>\n",
-       "      <td>Phospho@S</td>\n",
-       "      <td>5</td>\n",
-       "      <td>0</td>\n",
-       "      <td>6</td>\n",
-       "      <td>0.075327</td>\n",
-       "      <td>366.858877</td>\n",
-       "      <td>0</td>\n",
-       "      <td>6</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1</th>\n",
-       "      <td>7</td>\n",
-       "      <td>DPLAVDK</td>\n",
-       "      <td>2</td>\n",
-       "      <td>0.9</td>\n",
-       "      <td>379.208161</td>\n",
-       "      <td>-15.087100</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>6</td>\n",
-       "      <td>12</td>\n",
-       "      <td>0.199375</td>\n",
-       "      <td>367.043100</td>\n",
-       "      <td>6</td>\n",
-       "      <td>13</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>2</th>\n",
-       "      <td>7</td>\n",
-       "      <td>MGSLDSK</td>\n",
-       "      <td>2</td>\n",
-       "      <td>0.9</td>\n",
-       "      <td>409.161712</td>\n",
-       "      <td>-27.563500</td>\n",
-       "      <td>Phospho@S</td>\n",
-       "      <td>3</td>\n",
-       "      <td>12</td>\n",
-       "      <td>18</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>366.564438</td>\n",
-       "      <td>13</td>\n",
-       "      <td>16</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>3</th>\n",
-       "      <td>7</td>\n",
-       "      <td>SVSFSLK</td>\n",
-       "      <td>1</td>\n",
-       "      <td>0.9</td>\n",
-       "      <td>847.396112</td>\n",
-       "      <td>35.014110</td>\n",
-       "      <td>Phospho@S</td>\n",
-       "      <td>3</td>\n",
-       "      <td>18</td>\n",
-       "      <td>24</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>183.178171</td>\n",
-       "      <td>16</td>\n",
-       "      <td>25</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4</th>\n",
-       "      <td>7</td>\n",
-       "      <td>VSVSPGR</td>\n",
-       "      <td>2</td>\n",
-       "      <td>0.9</td>\n",
-       "      <td>431.167001</td>\n",
-       "      <td>-23.930850</td>\n",
-       "      <td>Phospho@S;Phospho@S</td>\n",
-       "      <td>2;4</td>\n",
-       "      <td>24</td>\n",
-       "      <td>30</td>\n",
-       "      <td>0.058050</td>\n",
-       "      <td>366.254833</td>\n",
-       "      <td>25</td>\n",
-       "      <td>34</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>5</th>\n",
-       "      <td>7</td>\n",
-       "      <td>YSLSPSK</td>\n",
-       "      <td>2</td>\n",
-       "      <td>0.9</td>\n",
-       "      <td>431.191326</td>\n",
-       "      <td>-6.428198</td>\n",
-       "      <td>Phospho@S</td>\n",
-       "      <td>4</td>\n",
-       "      <td>30</td>\n",
-       "      <td>36</td>\n",
-       "      <td>0.337745</td>\n",
-       "      <td>366.254509</td>\n",
-       "      <td>34</td>\n",
-       "      <td>41</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "   nAA sequence  charge  mobility  precursor_mz         rt  \\\n",
-       "0    7  AVVVSPK       2       0.9    390.206779 -22.849740   \n",
-       "1    7  DPLAVDK       2       0.9    379.208161 -15.087100   \n",
-       "2    7  MGSLDSK       2       0.9    409.161712 -27.563500   \n",
-       "3    7  SVSFSLK       1       0.9    847.396112  35.014110   \n",
-       "4    7  VSVSPGR       2       0.9    431.167001 -23.930850   \n",
-       "5    7  YSLSPSK       2       0.9    431.191326  -6.428198   \n",
-       "\n",
-       "                  mods mod_sites  frag_start_idx  frag_stop_idx   rt_norm  \\\n",
-       "0            Phospho@S         5               0              6  0.075327   \n",
-       "1                                              6             12  0.199375   \n",
-       "2            Phospho@S         3              12             18  0.000000   \n",
-       "3            Phospho@S         3              18             24  1.000000   \n",
-       "4  Phospho@S;Phospho@S       2;4              24             30  0.058050   \n",
-       "5            Phospho@S         4              30             36  0.337745   \n",
-       "\n",
-       "          ccs  flat_frag_start_idx  flat_frag_stop_idx  \n",
-       "0  366.858877                    0                   6  \n",
-       "1  367.043100                    6                  13  \n",
-       "2  366.564438                   13                  16  \n",
-       "3  183.178171                   16                  25  \n",
-       "4  366.254833                   25                  34  \n",
-       "5  366.254509                   34                  41  "
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "#| hide\n",
     "flat_lib.precursor_df"
@@ -622,7 +105,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -641,7 +124,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -665,529 +148,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "100%|██████████| 6/6 [00:00<00:00, 2457.12it/s]\n"
-     ]
-    },
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        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>b_z1</th>\n",
-       "      <th>b_z2</th>\n",
-       "      <th>y_z1</th>\n",
-       "      <th>y_z2</th>\n",
-       "      <th>b_modloss_z1</th>\n",
-       "      <th>b_modloss_z2</th>\n",
-       "      <th>y_modloss_z1</th>\n",
-       "      <th>y_modloss_z2</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.450362</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>2</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.106543</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.374123</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>3</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.069116</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.173858</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>5</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>6</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.515072</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>7</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.745664</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>8</th>\n",
-       "      <td>0.143703</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>9</th>\n",
-       "      <td>0.094888</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.377585</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>10</th>\n",
-       "      <td>0.054980</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>11</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>12</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.103734</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>13</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>14</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>15</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.092058</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>16</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>17</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>18</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>19</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.198974</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.774316</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>20</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.649715</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>21</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.882733</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.351781</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>22</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.400474</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>23</th>\n",
-       "      <td>0.244350</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.631000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>24</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.084908</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.328738</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>25</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.284129</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>26</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.276969</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.057554</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.262853</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>27</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.087439</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.061627</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>28</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>29</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>30</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.602346</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>31</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.141106</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.705295</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>32</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.108914</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.279959</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>33</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.492018</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>34</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>35</th>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "        b_z1      b_z2      y_z1      y_z2  b_modloss_z1  b_modloss_z2  \\\n",
-       "0   0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "1   0.000000  0.000000  0.450362  0.000000      0.000000           0.0   \n",
-       "2   0.000000  0.000000  0.106543  0.000000      0.000000           0.0   \n",
-       "3   0.000000  0.000000  0.069116  0.000000      0.000000           0.0   \n",
-       "4   0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "5   0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "6   0.000000  0.000000  0.000000  0.515072      0.000000           0.0   \n",
-       "7   0.000000  0.000000  0.745664  0.000000      0.000000           0.0   \n",
-       "8   0.143703  0.000000  1.000000  0.000000      0.000000           0.0   \n",
-       "9   0.094888  0.000000  0.377585  0.000000      0.000000           0.0   \n",
-       "10  0.054980  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "11  0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "12  0.000000  0.000000  0.103734  0.000000      0.000000           0.0   \n",
-       "13  0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "14  0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "15  0.000000  0.000000  0.092058  0.000000      0.000000           0.0   \n",
-       "16  0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "17  0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "18  0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "19  0.000000  0.000000  0.198974  0.000000      0.000000           0.0   \n",
-       "20  0.000000  0.000000  1.000000  0.000000      0.649715           0.0   \n",
-       "21  0.000000  0.000000  0.882733  0.000000      0.351781           0.0   \n",
-       "22  0.000000  0.000000  0.000000  0.000000      0.400474           0.0   \n",
-       "23  0.244350  0.000000  0.000000  0.000000      0.631000           0.0   \n",
-       "24  0.000000  0.000000  0.084908  0.000000      0.000000           0.0   \n",
-       "25  0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "26  0.000000  0.000000  0.276969  0.000000      0.057554           0.0   \n",
-       "27  0.000000  0.087439  1.000000  0.000000      0.061627           0.0   \n",
-       "28  0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "29  0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "30  0.000000  0.000000  0.602346  0.000000      0.000000           0.0   \n",
-       "31  0.000000  0.000000  0.141106  0.000000      0.000000           0.0   \n",
-       "32  0.000000  0.000000  0.108914  0.000000      0.000000           0.0   \n",
-       "33  0.000000  0.000000  0.492018  0.000000      0.000000           0.0   \n",
-       "34  0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "35  0.000000  0.000000  0.000000  0.000000      0.000000           0.0   \n",
-       "\n",
-       "    y_modloss_z1  y_modloss_z2  \n",
-       "0       0.000000           0.0  \n",
-       "1       1.000000           0.0  \n",
-       "2       0.374123           0.0  \n",
-       "3       0.173858           0.0  \n",
-       "4       0.000000           0.0  \n",
-       "5       0.000000           0.0  \n",
-       "6       0.000000           0.0  \n",
-       "7       0.000000           0.0  \n",
-       "8       0.000000           0.0  \n",
-       "9       0.000000           0.0  \n",
-       "10      0.000000           0.0  \n",
-       "11      0.000000           0.0  \n",
-       "12      1.000000           0.0  \n",
-       "13      0.000000           0.0  \n",
-       "14      0.000000           0.0  \n",
-       "15      0.000000           0.0  \n",
-       "16      0.000000           0.0  \n",
-       "17      0.000000           0.0  \n",
-       "18      0.000000           0.0  \n",
-       "19      0.774316           0.0  \n",
-       "20      0.000000           0.0  \n",
-       "21      0.000000           0.0  \n",
-       "22      0.000000           0.0  \n",
-       "23      0.000000           0.0  \n",
-       "24      0.328738           0.0  \n",
-       "25      0.284129           0.0  \n",
-       "26      0.262853           0.0  \n",
-       "27      0.000000           0.0  \n",
-       "28      0.000000           0.0  \n",
-       "29      0.000000           0.0  \n",
-       "30      1.000000           0.0  \n",
-       "31      0.705295           0.0  \n",
-       "32      0.279959           0.0  \n",
-       "33      0.000000           0.0  \n",
-       "34      0.000000           0.0  \n",
-       "35      0.000000           0.0  "
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "target = LibraryReaderBase()\n",
     "target.import_file(StringIO(tsv_str))\n",
@@ -1198,100 +159,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        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>mz</th>\n",
-       "      <th>intensity</th>\n",
-       "      <th>type</th>\n",
-       "      <th>loss_type</th>\n",
-       "      <th>charge</th>\n",
-       "      <th>position</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>609.300781</td>\n",
-       "      <td>0.450362</td>\n",
-       "      <td>121</td>\n",
-       "      <td>0</td>\n",
-       "      <td>1</td>\n",
-       "      <td>1</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1</th>\n",
-       "      <td>511.323853</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>121</td>\n",
-       "      <td>98</td>\n",
-       "      <td>1</td>\n",
-       "      <td>1</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>2</th>\n",
-       "      <td>510.232330</td>\n",
-       "      <td>0.106543</td>\n",
-       "      <td>121</td>\n",
-       "      <td>0</td>\n",
-       "      <td>1</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>3</th>\n",
-       "      <td>412.255432</td>\n",
-       "      <td>0.374123</td>\n",
-       "      <td>121</td>\n",
-       "      <td>98</td>\n",
-       "      <td>1</td>\n",
-       "      <td>2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4</th>\n",
-       "      <td>411.163940</td>\n",
-       "      <td>0.069116</td>\n",
-       "      <td>121</td>\n",
-       "      <td>0</td>\n",
-       "      <td>1</td>\n",
-       "      <td>3</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "           mz  intensity  type  loss_type  charge  position\n",
-       "0  609.300781   0.450362   121          0       1         1\n",
-       "1  511.323853   1.000000   121         98       1         1\n",
-       "2  510.232330   0.106543   121          0       1         2\n",
-       "3  412.255432   0.374123   121         98       1         2\n",
-       "4  411.163940   0.069116   121          0       1         3"
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Flatten original library to use it as a test input with target the original library\n",
     "flat_lib = SpecLibFlat(custom_fragment_df_columns=['type','charge','position','loss_type'])\n",
@@ -1303,100 +171,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        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>y_z2</th>\n",
-       "      <th>b_z2</th>\n",
-       "      <th>y_modloss_z1</th>\n",
-       "      <th>b_z1</th>\n",
-       "      <th>y_z1</th>\n",
-       "      <th>b_modloss_z1</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1</th>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>1.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.450362</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>2</th>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.374123</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.106543</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>3</th>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.173858</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.069116</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4</th>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.0</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "   y_z2  b_z2  y_modloss_z1  b_z1      y_z1  b_modloss_z1\n",
-       "0   0.0   0.0      0.000000   0.0  0.000000           0.0\n",
-       "1   0.0   0.0      1.000000   0.0  0.450362           0.0\n",
-       "2   0.0   0.0      0.374123   0.0  0.106543           0.0\n",
-       "3   0.0   0.0      0.173858   0.0  0.069116           0.0\n",
-       "4   0.0   0.0      0.000000   0.0  0.000000           0.0"
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "back_to_base = flat_lib.to_SpecLibBase()\n",
     "back_to_base.fragment_intensity_df.head()"
@@ -1406,25 +181,14 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "['_fragment_intensity_df', '_fragment_mz_df']"
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "back_to_base.available_dense_fragment_dfs()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1439,7 +203,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1450,7 +214,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1461,17 +225,62 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "# enable appending of flat libraries while making sure the flat_frag_start_idx is updated\n",
+    "\n",
+    "lib1 = SpecLibBase()\n",
+    "lib1.precursor_df = pd.DataFrame({\n",
+    "    'sequence': ['PEPTI', 'SEQUE'],\n",
+    "    'charge': [2, 3],\n",
+    "    'mod_sites': ['', ''],\n",
+    "    'mods': ['', ''],\n",
+    "})\n",
+    "lib1.calc_precursor_mz()\n",
+    "lib1.calc_fragment_mz_df()\n",
+    "lib1._fragment_intensity_df = lib1.fragment_mz_df.copy()\n",
+    "lib1._fragment_intensity_df.iloc[:] = 0\n",
+    "lib2 = lib1.copy()\n",
+    "lib2._fragment_intensity_df.iloc[:] = 1\n",
+    "\n",
+    "flatlib_1 = SpecLibFlat(min_fragment_intensity=0)\n",
+    "flatlib_1.parse_base_library(lib1, keep_original_frag_dfs=True)\n",
+    "flatlib_2 = SpecLibFlat(min_fragment_intensity=0)\n",
+    "flatlib_2.parse_base_library(lib2, keep_original_frag_dfs=True)\n",
+    "\n",
+    "flatlib_1.append(flatlib_2)\n",
+    "\n",
+    "assert flatlib_1.precursor_df.shape[0] == 4\n",
+    "assert flatlib_1.fragment_mz_df.shape[0] == 16\n",
+    "assert flatlib_1.fragment_df.shape[0] == np.prod(flatlib_1.fragment_mz_df.shape)\n",
+    "\n",
+    "assert np.all(flatlib_1.precursor_df['frag_start_idx'] == [0, 4, 8, 12])\n",
+    "assert np.all(flatlib_1.precursor_df['flat_frag_start_idx'] == [0, 16, 32, 48])\n",
+    "\n",
+    "assert np.all(flatlib_1.fragment_df['intensity'] == np.repeat([0, 1], 32))\n",
+    "assert np.all(flatlib_1.fragment_intensity_df.values.flatten() == np.repeat([0, 1], 32))"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "python3",
+   "display_name": "metaptcm",
    "language": "python",
    "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.5"
   }
  },
  "nbformat": 4,