From 77ebdf0cbfaaeb9f6ae135222e29c6a1d1256de0 Mon Sep 17 00:00:00 2001 From: jalew188 Date: Wed, 17 Jul 2024 15:57:57 +0200 Subject: [PATCH] #187 fix space PTMs --- docs/tutorials/basic_definations.ipynb | 50 +++++++++++++------------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/docs/tutorials/basic_definations.ipynb b/docs/tutorials/basic_definations.ipynb index 14cb9358..a7fe1ba8 100644 --- a/docs/tutorials/basic_definations.ipynb +++ b/docs/tutorials/basic_definations.ipynb @@ -648,7 +648,7 @@ "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." ] @@ -725,8 +725,8 @@ " 0.0\n", " \n", " \n", - " Acetyl@Protein N-term\n", - " Acetyl@Protein N-term\n", + " Acetyl@Protein_N-term\n", + " Acetyl@Protein_N-term\n", " 42.010565\n", " 42.0367\n", " H(2)C(2)O(1)\n", @@ -770,8 +770,8 @@ " 0.0\n", " \n", " \n", - " Acetyl@Any N-term\n", - " Acetyl@Any N-term\n", + " Acetyl@Any_N-term\n", + " Acetyl@Any_N-term\n", " 42.010565\n", " 42.0367\n", " H(2)C(2)O(1)\n", @@ -867,7 +867,7 @@ " H(6)C(4)N(2)O(2)\n", " 0.0\n", " \n", - " Post-translational\n", + " Multiple\n", " 121\n", " 1000000.0\n", " 114.042927\n", @@ -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", @@ -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", @@ -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", @@ -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", @@ -1013,7 +1013,7 @@ ], "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", @@ -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", @@ -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", @@ -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", @@ -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",