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Add TMT 10plex modifications #378

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Merged
GeorgWa merged 6 commits into from
Dec 29, 2025
Merged

Add TMT 10plex modifications #378

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d03fbbe
add tmt mods
GeorgWa Dec 26, 2025
5042aa6
fix attachment
GeorgWa Dec 26, 2025
c11a3cf
add tmt10
GeorgWa Dec 26, 2025
a83ddd3
fix tmt
GeorgWa Dec 29, 2025
7cef225
Merge remote-tracking branch 'origin/main' into tmt-mods
GeorgWa Dec 29, 2025
ac1c46e
fix: add placeholder atoms to TMT10plex@K and TMTpro@K SMILES
GeorgWa Dec 29, 2025
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10 changes: 8 additions & 2 deletions alphabase/constants/const_files/modification.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -1032,6 +1032,12 @@ TMT6plex@H 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label
TMT6plex@Protein_N-term 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0
TMT6plex@Any_N-term 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0
TMT6plex@K 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0
TMT10plex@T 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0
TMT10plex@S 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0
TMT10plex@H 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0
TMT10plex@Protein_N-term 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 0.0
TMT10plex@Any_N-term 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 C(=O)CCNC(=O)CN1C(C)CCCC1C 0.0
TMT10plex@K 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic label 737 CC1N(CC(NCCC(NCCCC[C@H](N([Fl])([Fl]))C(=O)[Ts])=O)=O)C(C)CCC1 0.0
BEMAD_C@C 120.0245 120.1701 H(8)C(4)O(2)S(1) 0.0 Chemical derivative 736 0.0
TMT2plex@H 225.155833 225.2921 H(20)C(11)13C(1)N(2)O(2) 0.0 Isotopic label 738 0.0
TMT2plex@S 225.155833 225.2921 H(20)C(11)13C(1)N(2)O(2) 0.0 Isotopic label 738 0.0
Expand Down Expand Up @@ -2697,8 +2703,8 @@ TMTpro@T 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2
TMTpro@S 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0
TMTpro@H 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0
TMTpro@Protein_N-term 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0
TMTpro@Any_N-term 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0
TMTpro@K 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 0.0
TMTpro@Any_N-term 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 C(=O)CCCNC(=O)CCCNC(=O)C1N(CC(C)C)CCC1 0.0
TMTpro@K 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2016 CC(CN1C(C(NCCC(NCCC(NCCCC[C@H](N([Fl])([Fl]))C(=O)[Ts])=O)=O)=O)CCC1)C 0.0
TMTpro_zero@S 295.189592 295.3773 H(25)C(15)N(3)O(3) 0.0 Chemical derivative 2017 0.0
TMTpro_zero@H 295.189592 295.3773 H(25)C(15)N(3)O(3) 0.0 Chemical derivative 2017 0.0
TMTpro_zero@Protein_N-term 295.189592 295.3773 H(25)C(15)N(3)O(3) 0.0 Chemical derivative 2017 0.0
Expand Down
4 changes: 4 additions & 0 deletions alphabase/constants/const_files/psm_reader.yaml
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Expand Up @@ -193,6 +193,10 @@ modification_mappings:
- 'K(148.1091)'
'mTRAQ:13C(6)15N(2)@Any_N-term':
- 'N-term(148.1091)'
'TMTpro@K':
- 'K(304.2071)'
'TMTpro@Any_N-term':
- 'N-term(304.2071)'

pfind:
reader_type: pfind
Expand Down
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