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#187 fix space PTMs
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@jalew188
jalew188 committed Jul 17, 2024
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50 changes: 25 additions & 25 deletions docs/tutorials/basic_definations.ipynb
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"source": [
"### Modifications\n",
"\n",
"In AlphaBase, we used `mod_name@aa` to represent a modification, the `mod_name` is from UniMod. We also used `mod_name@Protein N-term`, `mod_name@Any N-term` and `mod_name@Any C-term` for terminal modifications, which follow the UniMod terminal name schema.\n",
"In AlphaBase, we used `mod_name@aa` to represent a modification, the `mod_name` is from UniMod. We also used `mod_name@Protein_N-term`, `mod_name@Any_N-term` and `mod_name@Any_C-term` for terminal modifications, which follow the UniMod terminal name schema.\n",
"\n",
"The default modification TSV is stored in `alphabase/constants/const_files/modification.tsv`, users can add more modifications into the tsv file (only `mod_name` and `composition` colums are required). Please https://github.com/MannLabs/alphabase/blob/main/alphabase/constants/const_files/modification.tsv."
]
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" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Acetyl@Protein N-term</th>\n",
" <td>Acetyl@Protein N-term</td>\n",
" <th>Acetyl@Protein_N-term</th>\n",
" <td>Acetyl@Protein_N-term</td>\n",
" <td>42.010565</td>\n",
" <td>42.0367</td>\n",
" <td>H(2)C(2)O(1)</td>\n",
Expand Down Expand Up @@ -770,8 +770,8 @@
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Acetyl@Any N-term</th>\n",
" <td>Acetyl@Any N-term</td>\n",
" <th>Acetyl@Any_N-term</th>\n",
" <td>Acetyl@Any_N-term</td>\n",
" <td>42.010565</td>\n",
" <td>42.0367</td>\n",
" <td>H(2)C(2)O(1)</td>\n",
Expand Down Expand Up @@ -867,7 +867,7 @@
" <td>H(6)C(4)N(2)O(2)</td>\n",
" <td>0.0</td>\n",
" <td></td>\n",
" <td>Post-translational</td>\n",
" <td>Multiple</td>\n",
" <td>121</td>\n",
" <td>1000000.0</td>\n",
" <td>114.042927</td>\n",
Expand All @@ -883,10 +883,10 @@
" mod_name unimod_mass unimod_avge_mass \\\n",
"mod_name \n",
"Acetyl@T Acetyl@T 42.010565 42.0367 \n",
"Acetyl@Protein N-term Acetyl@Protein N-term 42.010565 42.0367 \n",
"Acetyl@Protein_N-term Acetyl@Protein_N-term 42.010565 42.0367 \n",
"Acetyl@S Acetyl@S 42.010565 42.0367 \n",
"Acetyl@C Acetyl@C 42.010565 42.0367 \n",
"Acetyl@Any N-term Acetyl@Any N-term 42.010565 42.0367 \n",
"Acetyl@Any_N-term Acetyl@Any_N-term 42.010565 42.0367 \n",
"... ... ... ... \n",
"TMTpro_zero@K TMTpro_zero@K 295.189592 295.3773 \n",
"TMTpro_zero@T TMTpro_zero@T 295.189592 295.3773 \n",
Expand All @@ -897,10 +897,10 @@
" composition unimod_modloss modloss_composition \\\n",
"mod_name \n",
"Acetyl@T H(2)C(2)O(1) 0.0 \n",
"Acetyl@Protein N-term H(2)C(2)O(1) 0.0 \n",
"Acetyl@Protein_N-term H(2)C(2)O(1) 0.0 \n",
"Acetyl@S H(2)C(2)O(1) 0.0 \n",
"Acetyl@C H(2)C(2)O(1) 0.0 \n",
"Acetyl@Any N-term H(2)C(2)O(1) 0.0 \n",
"Acetyl@Any_N-term H(2)C(2)O(1) 0.0 \n",
"... ... ... ... \n",
"TMTpro_zero@K H(25)C(15)N(3)O(3) 0.0 \n",
"TMTpro_zero@T H(25)C(15)N(3)O(3) 0.0 \n",
Expand All @@ -911,24 +911,24 @@
" classification unimod_id modloss_importance \\\n",
"mod_name \n",
"Acetyl@T Post-translational 1 0.0 \n",
"Acetyl@Protein N-term Post-translational 1 0.0 \n",
"Acetyl@Protein_N-term Post-translational 1 0.0 \n",
"Acetyl@S Post-translational 1 0.0 \n",
"Acetyl@C Post-translational 1 0.0 \n",
"Acetyl@Any N-term Multiple 1 0.0 \n",
"Acetyl@Any_N-term Multiple 1 0.0 \n",
"... ... ... ... \n",
"TMTpro_zero@K Chemical derivative 2017 0.0 \n",
"TMTpro_zero@T Chemical derivative 2017 0.0 \n",
"Andro-H2O@C Chemical derivative 2025 0.0 \n",
"His+O(2)@H Post-translational 2027 0.0 \n",
"GlyGly@K Post-translational 121 1000000.0 \n",
"GlyGly@K Multiple 121 1000000.0 \n",
"\n",
" mass modloss_original modloss \n",
"mod_name \n",
"Acetyl@T 42.010565 0.0 0.0 \n",
"Acetyl@Protein N-term 42.010565 0.0 0.0 \n",
"Acetyl@Protein_N-term 42.010565 0.0 0.0 \n",
"Acetyl@S 42.010565 0.0 0.0 \n",
"Acetyl@C 42.010565 0.0 0.0 \n",
"Acetyl@Any N-term 42.010565 0.0 0.0 \n",
"Acetyl@Any_N-term 42.010565 0.0 0.0 \n",
"... ... ... ... \n",
"TMTpro_zero@K 295.189592 0.0 0.0 \n",
"TMTpro_zero@T 295.189592 0.0 0.0 \n",
Expand Down Expand Up @@ -978,7 +978,7 @@
"source": [
"from alphabase.constants.modification import calc_modification_mass\n",
"sequence = 'MACDEFG'\n",
"mod_names = ['Acetyl@Any N-term', 'Carbamidomethyl@C']\n",
"mod_names = ['Acetyl@Any_N-term', 'Carbamidomethyl@C']\n",
"mod_sites = [0,3]\n",
"calc_modification_mass(\n",
" nAA=len(sequence),\n",
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],
"source": [
"sequence = 'MAKDEFG'\n",
"mod_names = ['Acetyl@Any N-term', 'Oxidation@M']\n",
"mod_names = ['Acetyl@Any_N-term', 'Oxidation@M']\n",
"mod_sites = [0,1]\n",
"calc_modification_mass(\n",
" nAA=len(sequence),\n",
Expand Down Expand Up @@ -1090,8 +1090,8 @@
"calc_mod_masses_for_same_len_seqs(\n",
" nAA=7,\n",
" mod_names_list=[\n",
" ['Acetyl@Any N-term', 'Carbamidomethyl@C'],\n",
" ['Acetyl@Any N-term', 'Oxidation@M'],\n",
" ['Acetyl@Any_N-term', 'Carbamidomethyl@C'],\n",
" ['Acetyl@Any_N-term', 'Oxidation@M'],\n",
" ['GlyGly@K', 'Dimethyl@K'],\n",
" ],\n",
" mod_sites_list=[\n",
Expand Down Expand Up @@ -1143,8 +1143,8 @@
"mod_masses = calc_mod_masses_for_same_len_seqs(\n",
" nAA=7,\n",
" mod_names_list=[\n",
" ['Acetyl@Any N-term', 'Carbamidomethyl@C'],\n",
" ['Acetyl@Any N-term', 'Oxidation@M'],\n",
" ['Acetyl@Any_N-term', 'Carbamidomethyl@C'],\n",
" ['Acetyl@Any_N-term', 'Oxidation@M'],\n",
" ['GlyGly@K', 'Dimethyl@K'],\n",
" ],\n",
" mod_sites_list=[\n",
Expand Down Expand Up @@ -1225,8 +1225,8 @@
"peptide_masses = calc_peptide_masses_for_same_len_seqs(\n",
" ['MACDEFG', 'MAKDEFG', 'MAKDEFR'],\n",
" mod_list=[\n",
" 'Acetyl@Any N-term;Carbamidomethyl@C',\n",
" 'Acetyl@Any N-term;Oxidation@M',\n",
" 'Acetyl@Any_N-term;Carbamidomethyl@C',\n",
" 'Acetyl@Any_N-term;Oxidation@M',\n",
" 'GlyGly@K;Dimethyl@K',\n",
" ],\n",
")\n",
Expand Down Expand Up @@ -1254,8 +1254,8 @@
"b_masses, y_masses, peptide_masses = calc_b_y_and_peptide_masses_for_same_len_seqs(\n",
" ['MACDEFG', 'MAKDEFG', 'MAKDEFR'],\n",
" mod_list=[\n",
" ['Acetyl@Any N-term', 'Carbamidomethyl@C'],\n",
" ['Acetyl@Any N-term', 'Oxidation@M'],\n",
" ['Acetyl@Any_N-term', 'Carbamidomethyl@C'],\n",
" ['Acetyl@Any_N-term', 'Oxidation@M'],\n",
" ['GlyGly@K', 'Dimethyl@K'],\n",
" ],\n",
" site_list=[\n",
Expand Down

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