diff --git a/docs/nbs/library_reader.ipynb b/docs/nbs/library_reader.ipynb index b31554f6..499d5375 100644 --- a/docs/nbs/library_reader.ipynb +++ b/docs/nbs/library_reader.ipynb @@ -2065,7 +2065,7 @@ " 4\n", " 2.957368\n", " NaN\n", - " Dimethyl:2H(4)@Any N-term\n", + " Dimethyl:2H(4)@Any_N-term\n", " 0\n", " 9\n", " 0\n", @@ -2080,7 +2080,7 @@ " 3\n", " 10.904905\n", " NaN\n", - " Dimethyl:2H(4)@Any N-term\n", + " Dimethyl:2H(4)@Any_N-term\n", " 0\n", " 7\n", " 8\n", @@ -2095,8 +2095,8 @@ ], "text/plain": [ " sequence charge rt mobility mods \\\n", - "0 EDTEEHHLR 4 2.957368 NaN Dimethyl:2H(4)@Any N-term \n", - "1 MQHLIAR 3 10.904905 NaN Dimethyl:2H(4)@Any N-term \n", + "0 EDTEEHHLR 4 2.957368 NaN Dimethyl:2H(4)@Any_N-term \n", + "1 MQHLIAR 3 10.904905 NaN Dimethyl:2H(4)@Any_N-term \n", "\n", " mod_sites nAA frag_start_idx frag_stop_idx rt_norm precursor_mz ccs \n", "0 0 9 0 8 0.271196 300.150369 NaN \n", diff --git a/nbs_tests/constants/modification.ipynb b/nbs_tests/constants/modification.ipynb index 9a68d9bb..a3996002 100644 --- a/nbs_tests/constants/modification.ipynb +++ b/nbs_tests/constants/modification.ipynb @@ -156,8 +156,8 @@ " 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", @@ -570,8 +570,8 @@ " 0.0\n", " \n", " \n", - " Oxidation@G^Any C-term\n", - " Oxidation@G^Any C-term\n", + " Oxidation@G^Any_C-term\n", + " Oxidation@G^Any_C-term\n", " 15.994915\n", " 15.9994\n", " O(1)\n", @@ -716,7 +716,7 @@ "Acetyl@Y Acetyl@Y 42.010565 \n", "Acetyl@R Acetyl@R 42.010565 \n", "ICAT-G@C ICAT-G@C 486.251206 \n", - "Oxidation@G^Any C-term Oxidation@G^Any C-term 15.994915 \n", + "Oxidation@G^Any_C-term Oxidation@G^Any_C-term 15.994915 \n", "Hex@C Hex@C 162.052824 \n", "Hex@T Hex@T 162.052824 \n", "Hex@N Hex@N 162.052824 \n", @@ -733,7 +733,7 @@ "Acetyl@Y 42.0367 H(2)C(2)O(1) \n", "Acetyl@R 42.0367 H(2)C(2)O(1) \n", "ICAT-G@C 486.6253 H(38)C(22)N(4)O(6)S(1) \n", - "Oxidation@G^Any C-term 15.9994 O(1) \n", + "Oxidation@G^Any_C-term 15.9994 O(1) \n", "Hex@C 162.1406 H(10)C(6)O(5) \n", "Hex@T 162.1406 H(10)C(6)O(5) \n", "Hex@N 162.1406 H(10)C(6)O(5) \n", @@ -750,7 +750,7 @@ "Acetyl@Y 0.000000 \n", "Acetyl@R 0.000000 \n", "ICAT-G@C 0.000000 \n", - "Oxidation@G^Any C-term 0.000000 \n", + "Oxidation@G^Any_C-term 0.000000 \n", "Hex@C 0.000000 \n", "Hex@T 162.052824 H(10)C(6)O(5) \n", "Hex@N 162.052824 H(10)C(6)O(5) \n", @@ -767,7 +767,7 @@ "Acetyl@Y Chemical derivative 1 \n", "Acetyl@R Artefact 1 \n", "ICAT-G@C Isotopic label 8 \n", - "Oxidation@G^Any C-term Pre-translational 35 \n", + "Oxidation@G^Any_C-term Pre-translational 35 \n", "Hex@C Other glycosylation 41 \n", "Hex@T O-linked glycosylation 41 \n", "Hex@N N-linked glycosylation 41 \n", @@ -784,7 +784,7 @@ "Acetyl@Y 0.0 42.010565 \n", "Acetyl@R 0.0 42.010565 \n", "ICAT-G@C 0.0 486.251206 \n", - "Oxidation@G^Any C-term 0.0 15.994915 \n", + "Oxidation@G^Any_C-term 0.0 15.994915 \n", "Hex@C 0.0 162.052823 \n", "Hex@T 0.0 162.052823 \n", "Hex@N 0.0 162.052823 \n", @@ -801,7 +801,7 @@ "Acetyl@Y 0.000000 0.0 \n", "Acetyl@R 0.000000 0.0 \n", "ICAT-G@C 0.000000 0.0 \n", - "Oxidation@G^Any C-term 0.000000 0.0 \n", + "Oxidation@G^Any_C-term 0.000000 0.0 \n", "Hex@C 0.000000 0.0 \n", "Hex@T 162.052823 0.0 \n", "Hex@N 162.052823 0.0 \n", diff --git a/nbs_tests/psm_reader/alphapept_reader.ipynb b/nbs_tests/psm_reader/alphapept_reader.ipynb index f19aed9c..d1af6d84 100644 --- a/nbs_tests/psm_reader/alphapept_reader.ipynb +++ b/nbs_tests/psm_reader/alphapept_reader.ipynb @@ -76,7 +76,7 @@ " 'Phospho@S': 'pS',\n", " 'Phospho@T': 'pT',\n", " 'Phospho@Y': 'pY',\n", - " 'Acetyl@Protein N-term': 'a'}" + " 'Acetyl@Protein_N-term': 'a'}" ] }, "execution_count": null, diff --git a/nbs_tests/psm_reader/maxquant_reader.ipynb b/nbs_tests/psm_reader/maxquant_reader.ipynb index 7d5fbced..90c9c5f0 100644 --- a/nbs_tests/psm_reader/maxquant_reader.ipynb +++ b/nbs_tests/psm_reader/maxquant_reader.ipynb @@ -75,7 +75,7 @@ "text/plain": [ "{'Dimethyl@K': ['K(Dimethyl)'],\n", " 'Dimethyl@R': ['R(Dimethyl)'],\n", - " 'Dimethyl@Any N-term': ['(Dimethyl)'],\n", + " 'Dimethyl@Any_N-term': ['(Dimethyl)'],\n", " 'Acetyl@Protein_N-term': ['_(Acetyl (Protein_N-term))', '_(ac)'],\n", " 'Carbamidomethyl@C': ['C(Carbamidomethyl (C))', 'C(Carbamidomethyl)'],\n", " 'Oxidation@M': ['M(Oxidation)', 'M(Oxidation (M))', 'M(ox)'],\n",