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Merge pull request #21 from pgarrett-scripps/main
corrected reference molecules entries
2 parents 8eade69 + f9703f3 commit e196ee7

3 files changed

Lines changed: 47 additions & 22 deletions

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‎implementations/python/mzpaf/data/reference_molecules.json‎

Lines changed: 32 additions & 7 deletions
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@@ -75,7 +75,7 @@
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C2[13C6]N1H15",
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"ion_mz": 122.147855
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"ion_mz": 132.147855
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},
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"TMT133N": {
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"label_type": "TMT",
@@ -131,7 +131,7 @@
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"TMT6plex": {
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"label_type": "TMT6plex",
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"molecule_type": "reporter+balance",
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"chemical_formula": "C8[13C5]H20N1[15N1]O2",
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"chemical_formula": "C8[13C4]H20N1[15N1]O2",
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"neutral_mass": 229.162932,
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"ion_mz": 230.17020847
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},
@@ -219,13 +219,13 @@
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"TMT127C-ETD": {
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C6[13C1]N1H15",
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"chemical_formula": "C7N1H15",
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"ion_mz": 114.127725
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},
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"TMT128N-ETD": {
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C6[13C1][15N1]H15",
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"chemical_formula": "C7[15N1]H15",
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"ion_mz": 115.12476
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},
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"TMT128C-ETD": {
@@ -243,13 +243,13 @@
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"TMT129C-ETD": {
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C4[13C3]N1H15",
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"chemical_formula": "C5[13C2]N1H15",
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"ion_mz": 116.134433
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},
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"TMT130N-ETD": {
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C4[13C3][15N1]H15",
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"chemical_formula": "C5[13C2][15N1]H15",
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"ion_mz": 117.131468
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},
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"TMT130C-ETD": {
@@ -267,7 +267,7 @@
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"TMT131C-ETD": {
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C2[13C5]N1H15",
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"chemical_formula": "C3[13C4]N1H15",
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"ion_mz": 118.141141
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},
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"sidechain_A": {
@@ -379,5 +379,30 @@
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"molecule_type": "sidechain",
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"chemical_formula": "C7H7O1",
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"neutral_mass": 107.049690
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},
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"Cytosine": {
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"molecule_type": "nucleobase",
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"chemical_formula": "C4H5N3O",
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"ion_mz": 112.050538
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},
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"Adenine": {
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"molecule_type": "nucleobase",
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"chemical_formula": "C5H5N5",
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"ion_mz": 136.061772
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},
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"Guanine": {
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"molecule_type": "nucleobase",
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"chemical_formula": "C5H5N5O",
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"ion_mz": 152.056686
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},
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"Uracil": {
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"molecule_type": "nucleobase",
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"chemical_formula": "C4H4N2O2",
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"ion_mz": 113.034554
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},
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"Thymine": {
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"molecule_type": "nucleobase",
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"chemical_formula": "C5H6N2O2",
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"ion_mz": 127.050204
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}
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}

‎specification/reference_data/reference_molecules.json‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -75,7 +75,7 @@
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C2[13C6]N1H15",
78-
"ion_mz": 122.147855
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"ion_mz": 132.147855
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},
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"TMT133N": {
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"label_type": "TMT",
@@ -131,7 +131,7 @@
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"TMT6plex": {
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"label_type": "TMT6plex",
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"molecule_type": "reporter+balance",
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"chemical_formula": "C8[13C5]H20N1[15N1]O2",
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"chemical_formula": "C8[13C4]H20N1[15N1]O2",
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"neutral_mass": 229.162932,
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"ion_mz": 230.17020847
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},
@@ -219,13 +219,13 @@
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"TMT127C-ETD": {
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C6[13C1]N1H15",
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"chemical_formula": "C7N1H15",
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"ion_mz": 114.127725
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},
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"TMT128N-ETD": {
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C6[13C1][15N1]H15",
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"chemical_formula": "C7[15N1]H15",
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"ion_mz": 115.12476
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},
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"TMT128C-ETD": {
@@ -243,13 +243,13 @@
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"TMT129C-ETD": {
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C4[13C3]N1H15",
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"chemical_formula": "C5[13C2]N1H15",
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"ion_mz": 116.134433
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},
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"TMT130N-ETD": {
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C4[13C3][15N1]H15",
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"chemical_formula": "C5[13C2][15N1]H15",
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"ion_mz": 117.131468
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},
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"TMT130C-ETD": {
@@ -267,7 +267,7 @@
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"TMT131C-ETD": {
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"label_type": "TMT",
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"molecule_type": "reporter",
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"chemical_formula": "C2[13C5]N1H15",
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"chemical_formula": "C3[13C4]N1H15",
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"ion_mz": 118.141141
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},
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"sidechain_A": {
@@ -405,4 +405,4 @@
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"chemical_formula": "C5H6N2O2",
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"ion_mz": 127.050204
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}
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}
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}

‎specification/reference_data/reference_molecules.md‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@
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| TMT131N | TMT | reporter | C4[13C4][15N1]H15 | 131.138 | |
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| TMT131C | TMT | reporter | C3[13C5]N1H15 | 131.144 | |
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| TMT132N | TMT | reporter | C3[13C5][15N1]H15 | 132.142 | |
15-
| TMT132C | TMT | reporter | C2[13C6]N1H15 | 122.148 | |
15+
| TMT132C | TMT | reporter | C2[13C6]N1H15 | 132.148 | |
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| TMT133N | TMT | reporter | C2[13C6][15N1]H15 | 133.145 | |
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| TMT133C | TMT | reporter | C1[13C7]N1H15 | 133.151 | |
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| TMT134N | TMT | reporter | C1[13C7][15N1]H15 | 134.148 | |
@@ -21,7 +21,7 @@
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| TMTzero | TMTzero | reporter+balance | C12H20N2O2 | 225.16 | 224.152 |
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| TMTpro_zero | TMTpro_zero | reporter+balance | C15H25N3O3 | 296.197 | 295.19 |
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| TMT2plex | TMT2plex | reporter+balance | C11[13C1]H20N2O2 | 226.163 | 225.156 |
24-
| TMT6plex | TMT6plex | reporter+balance | C8[13C5]H20N1[15N1]O2 | 230.17 | 229.163 |
24+
| TMT6plex | TMT6plex | reporter+balance | C8[13C4]H20N1[15N1]O2 | 230.17 | 229.163 |
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| TMTpro | TMTpro | reporter+balance | C8[13C7]H25[15N2]N1O3 | 305.214 | 304.207 |
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| iTRAQ113 | iTRAQ | reporter | C6N2H12 | 113.108 | |
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| iTRAQ114 | iTRAQ | reporter | C5[13C1]N2H12 | 114.111 | |
@@ -35,15 +35,15 @@
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| iTRAQ8plex | iTRAQ8plex | reporter+balance | C7[13C7]N3[15N1]O3H24 | 305.213 | 304.205 |
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| TMT126-ETD | TMT | reporter | C7N1H15 | 114.128 | |
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| TMT127N-ETD | TMT | reporter | C7[15N1]H15 | 115.125 | |
38-
| TMT127C-ETD | TMT | reporter | C6[13C1]N1H15 | 114.128 | |
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| TMT128N-ETD | TMT | reporter | C6[13C1][15N1]H15 | 115.125 | |
38+
| TMT127C-ETD | TMT | reporter | C7N1H15 | 114.128 | |
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| TMT128N-ETD | TMT | reporter | C7[15N1]H15 | 115.125 | |
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| TMT128C-ETD | TMT | reporter | C5[13C2]N1H15 | 116.134 | |
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| TMT129N-ETD | TMT | reporter | C5[13C2][15N1]H15 | 117.131 | |
42-
| TMT129C-ETD | TMT | reporter | C4[13C3]N1H15 | 116.134 | |
43-
| TMT130N-ETD | TMT | reporter | C4[13C3][15N1]H15 | 117.131 | |
42+
| TMT129C-ETD | TMT | reporter | C5[13C2]N1H15 | 116.134 | |
43+
| TMT130N-ETD | TMT | reporter | C5[13C2][15N1]H15 | 117.131 | |
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| TMT130C-ETD | TMT | reporter | C3[13C4]N1H15 | 118.141 | |
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| TMT131N-ETD | TMT | reporter | C3[13C4][15N1]H15 | 119.138 | |
46-
| TMT131C-ETD | TMT | reporter | C2[13C5]N1H15 | 118.141 | |
46+
| TMT131C-ETD | TMT | reporter | C3[13C4]N1H15 | 118.141 | |
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| sidechain_A | | sidechain | C1H3 | | 15.0235 |
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| sidechain_C | | sidechain | C1H3S1 | | 46.9955 |
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| sidechain_D | | sidechain | C2H2O2 | | 58.0055 |

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