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HUPO-PSI · Sep 13, 2024 · 7432cf0 · 7432cf0
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diff --git a/implementations/python/mzpaf/data/reference_molecules.json b/implementations/python/mzpaf/data/reference_molecules.json
@@ -269,5 +269,115 @@
     "molecule_type": "reporter",
     "chemical_formula": "C2[13C5]N1H15",
     "ion_mz": 118.141141
+  },
+  "sidechain_A": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C1H3",
+    "neutral_mass": 15.023475
+  },
+  "sidechain_C": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C1H3S1",
+    "neutral_mass": 46.995546
+  },
+  "sidechain_D": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C2H2O2",
+    "neutral_mass": 58.005479
+  },
+  "sidechain_E": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C3H4O2",
+    "neutral_mass": 72.021129
+  },
+  "sidechain_F": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C7H7",
+    "neutral_mass": 91.054775
+  },
+  "sidechain_G": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "H1",
+    "neutral_mass": 1.007825
+  },
+  "sidechain_H": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C4H5N2",
+    "neutral_mass": 81.045273
+  },
+  "sidechain_I": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C4H9",
+    "neutral_mass": 57.070425
+  },
+  "sidechain_J": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C4H9",
+    "neutral_mass": 57.070425
+  },
+  "sidechain_K": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C4H10N1",
+    "neutral_mass": 72.081324
+  },
+  "sidechain_L": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C4H9",
+    "neutral_mass": 57.070425
+  },
+  "sidechain_M": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C3H7S1",
+    "neutral_mass": 75.026846
+  },
+  "sidechain_N": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C2H4N1O1",
+    "neutral_mass": 58.029289
+  },
+  "sidechain_O": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C9H17N2O1",
+    "neutral_mass": 169.134088
+  },
+  "sidechain_Q": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C3H6N1O1",
+    "neutral_mass": 72.044939
+  },
+  "sidechain_R": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C4H10N3",
+    "neutral_mass": 100.087472
+  },
+  "sidechain_S": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C1H3O1",
+    "neutral_mass": 31.018390
+  },
+  "sidechain_T": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C2H5O1",
+    "neutral_mass": 45.034040
+  },
+  "sidechain_U": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C1H3Se1",
+    "neutral_mass": 94.939997
+  },
+  "sidechain_V": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C3H7",
+    "neutral_mass": 43.054775
+  },
+  "sidechain_W": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C9H8N1",
+    "neutral_mass": 130.065674
+  },
+  "sidechain_Y": {
+    "molecule_type": "sidechain",
+    "chemical_formula": "C7H7O1",
+    "neutral_mass": 107.049690
   }
 }
diff --git a/specification/reference_data/reference_molecules.md b/specification/reference_data/reference_molecules.md
@@ -1,4 +1,4 @@
-|     name    | label_type   | molecule_type    | chemical_formula      |   ion_mz |   neutral_mass |
+|             | label_type   | molecule_type    | chemical_formula      |   ion_mz |   neutral_mass |
 |:------------|:-------------|:-----------------|:----------------------|---------:|---------------:|
 | TMT126      | TMT          | reporter         | C8N1H15               |  126.128 |                |
 | TMT127N     | TMT          | reporter         | C8[15N1]H15           |  127.125 |                |
@@ -18,11 +18,11 @@
 | TMT134N     | TMT          | reporter         | C1[13C7][15N1]H15     |  134.148 |                |
 | TMT134C     | TMT          | reporter         | [13C8]N1H15           |  134.155 |                |
 | TMT135N     | TMT          | reporter         | [13C8][15N1]H15       |  135.152 |                |
-| TMTzero     | TMTzero      | reporter+balance | C12H20N2O2            |  225.16  |        224.152 |
-| TMTpro_zero | TMTpro_zero  | reporter+balance | C15H25N3O3            |  296.197 |        295.19  |
-| TMT2plex    | TMT2plex     | reporter+balance | C11[13C1]H20N2O2      |  226.163 |        225.156 |
-| TMT6plex    | TMT6plex     | reporter+balance | C8[13C5]H20N1[15N1]O2 |  230.17  |        229.163 |
-| TMTpro      | TMTpro       | reporter+balance | C8[13C7]H25[15N2]N1O3 |  305.214 |        304.207 |
+| TMTzero     | TMTzero      | reporter+balance | C12H20N2O2            |  225.16  |      224.152   |
+| TMTpro_zero | TMTpro_zero  | reporter+balance | C15H25N3O3            |  296.197 |      295.19    |
+| TMT2plex    | TMT2plex     | reporter+balance | C11[13C1]H20N2O2      |  226.163 |      225.156   |
+| TMT6plex    | TMT6plex     | reporter+balance | C8[13C5]H20N1[15N1]O2 |  230.17  |      229.163   |
+| TMTpro      | TMTpro       | reporter+balance | C8[13C7]H25[15N2]N1O3 |  305.214 |      304.207   |
 | iTRAQ113    | iTRAQ        | reporter         | C6N2H12               |  113.108 |                |
 | iTRAQ114    | iTRAQ        | reporter         | C5[13C1]N2H12         |  114.111 |                |
 | iTRAQ115    | iTRAQ        | reporter         | C5[13C1]N1[15N1]H12   |  115.108 |                |
@@ -31,8 +31,8 @@
 | iTRAQ118    | iTRAQ        | reporter         | C3[13C3][15N2]H12     |  118.112 |                |
 | iTRAQ119    | iTRAQ        | reporter         | C2[13C4][15N2]H12     |  119.115 |                |
 | iTRAQ121    | iTRAQ        | reporter         | [13C6][15N2]H12       |  121.122 |                |
-| iTRAQ4plex  | iTRAQ4plex   | reporter+balance | C4[13C3]N1[15N1]O1H12 |  145.109 |        144.102 |
-| iTRAQ8plex  | iTRAQ8plex   | reporter+balance | C7[13C7]N3[15N1]O3H24 |  305.213 |        304.205 |
+| iTRAQ4plex  | iTRAQ4plex   | reporter+balance | C4[13C3]N1[15N1]O1H12 |  145.109 |      144.102   |
+| iTRAQ8plex  | iTRAQ8plex   | reporter+balance | C7[13C7]N3[15N1]O3H24 |  305.213 |      304.205   |
 | TMT126-ETD  | TMT          | reporter         | C7N1H15               |  114.128 |                |
 | TMT127N-ETD | TMT          | reporter         | C7[15N1]H15           |  115.125 |                |
 | TMT127C-ETD | TMT          | reporter         | C6[13C1]N1H15         |  114.128 |                |
@@ -44,3 +44,25 @@
 | TMT130C-ETD | TMT          | reporter         | C3[13C4]N1H15         |  118.141 |                |
 | TMT131N-ETD | TMT          | reporter         | C3[13C4][15N1]H15     |  119.138 |                |
 | TMT131C-ETD | TMT          | reporter         | C2[13C5]N1H15         |  118.141 |                |
+| sidechain_A |              | sidechain        | C1H3                  |          |       15.0235  |
+| sidechain_C |              | sidechain        | C1H3S1                |          |       46.9955  |
+| sidechain_D |              | sidechain        | C2H2O2                |          |       58.0055  |
+| sidechain_E |              | sidechain        | C3H4O2                |          |       72.0211  |
+| sidechain_F |              | sidechain        | C7H7                  |          |       91.0548  |
+| sidechain_G |              | sidechain        | H1                    |          |        1.00782 |
+| sidechain_H |              | sidechain        | C4H5N2                |          |       81.0453  |
+| sidechain_I |              | sidechain        | C4H9                  |          |       57.0704  |
+| sidechain_J |              | sidechain        | C4H9                  |          |       57.0704  |
+| sidechain_K |              | sidechain        | C4H10N1               |          |       72.0813  |
+| sidechain_L |              | sidechain        | C4H9                  |          |       57.0704  |
+| sidechain_M |              | sidechain        | C3H7S1                |          |       75.0268  |
+| sidechain_N |              | sidechain        | C2H4N1O1              |          |       58.0293  |
+| sidechain_O |              | sidechain        | C9H17N2O1             |          |      169.134   |
+| sidechain_Q |              | sidechain        | C3H6N1O1              |          |       72.0449  |
+| sidechain_R |              | sidechain        | C4H10N3               |          |      100.087   |
+| sidechain_S |              | sidechain        | C1H3O1                |          |       31.0184  |
+| sidechain_T |              | sidechain        | C2H5O1                |          |       45.034   |
+| sidechain_U |              | sidechain        | C1H3Se1               |          |       94.94    |
+| sidechain_V |              | sidechain        | C3H7                  |          |       43.0548  |
+| sidechain_W |              | sidechain        | C9H8N1                |          |      130.066   |
+| sidechain_Y |              | sidechain        | C7H7O1                |          |      107.05    |