From d03fbbecc092ead3b0b1b3a7999dc5f129c1d1c8 Mon Sep 17 00:00:00 2001 From: GeorgWa Date: Fri, 26 Dec 2025 23:05:34 +0100 Subject: [PATCH 1/5] add tmt mods --- alphabase/constants/const_files/modification.tsv | 4 ++-- alphabase/constants/const_files/psm_reader.yaml | 4 ++++ 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/alphabase/constants/const_files/modification.tsv b/alphabase/constants/const_files/modification.tsv index ba29fd28..af59f458 100644 --- a/alphabase/constants/const_files/modification.tsv +++ b/alphabase/constants/const_files/modification.tsv @@ -2697,8 +2697,8 @@ 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 CC(CN1C(C(NCCC(NCCC(N)=O)=O)=O)CCC1)C 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)C(=O)O)=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 diff --git a/alphabase/constants/const_files/psm_reader.yaml b/alphabase/constants/const_files/psm_reader.yaml index 21633a4a..98959217 100644 --- a/alphabase/constants/const_files/psm_reader.yaml +++ b/alphabase/constants/const_files/psm_reader.yaml @@ -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 From 5042aa68b9bded8b7f752b7377331b9ed1063c88 Mon Sep 17 00:00:00 2001 From: GeorgWa Date: Fri, 26 Dec 2025 23:13:13 +0100 Subject: [PATCH 2/5] fix attachment --- alphabase/constants/const_files/modification.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/alphabase/constants/const_files/modification.tsv b/alphabase/constants/const_files/modification.tsv index af59f458..2cbfc9ca 100644 --- a/alphabase/constants/const_files/modification.tsv +++ b/alphabase/constants/const_files/modification.tsv @@ -2697,7 +2697,7 @@ 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 CC(CN1C(C(NCCC(NCCC(N)=O)=O)=O)CCC1)C 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)C(=O)O)=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 From c11a3cf829583c071e8c835ef3666a6b6920015d Mon Sep 17 00:00:00 2001 From: GeorgWa Date: Fri, 26 Dec 2025 23:36:16 +0100 Subject: [PATCH 3/5] add tmt10 --- alphabase/constants/const_files/modification.tsv | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/alphabase/constants/const_files/modification.tsv b/alphabase/constants/const_files/modification.tsv index 2cbfc9ca..2628490e 100644 --- a/alphabase/constants/const_files/modification.tsv +++ b/alphabase/constants/const_files/modification.tsv @@ -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)CCCNC(=O)CN1C(C)CCC1C 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)C(=O)O)=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 From a83ddd3ba7997b0b5529a5ca814ce547e51440dc Mon Sep 17 00:00:00 2001 From: GeorgWa Date: Mon, 29 Dec 2025 16:45:46 +0100 Subject: [PATCH 4/5] fix tmt --- alphabase/constants/const_files/modification.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/alphabase/constants/const_files/modification.tsv b/alphabase/constants/const_files/modification.tsv index 2628490e..f4eac533 100644 --- a/alphabase/constants/const_files/modification.tsv +++ b/alphabase/constants/const_files/modification.tsv @@ -1036,7 +1036,7 @@ TMT10plex@T 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic labe 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)CCCNC(=O)CN1C(C)CCC1C 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)C(=O)O)=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 From ac1c46e2bdfb6c4f7608954b33e107be072633ce Mon Sep 17 00:00:00 2001 From: GeorgWa Date: Mon, 29 Dec 2025 18:56:47 +0100 Subject: [PATCH 5/5] fix: add placeholder atoms to TMT10plex@K and TMTpro@K SMILES MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The SMILES were missing [Fl] (N-term) and [Ts] (C-term) placeholders required by modify_amino_acid validation. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude --- alphabase/constants/const_files/modification.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/alphabase/constants/const_files/modification.tsv b/alphabase/constants/const_files/modification.tsv index 48a8adba..533f5217 100644 --- a/alphabase/constants/const_files/modification.tsv +++ b/alphabase/constants/const_files/modification.tsv @@ -1037,7 +1037,7 @@ TMT10plex@S 229.162932 229.2634 H(20)C(8)13C(4)N(1)15N(1)O(2) 0.0 Isotopic labe 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)C(=O)O)=O)=O)C(C)CCC1 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 @@ -2704,7 +2704,7 @@ TMTpro@S 304.207146 304.3127 H(25)C(8)13C(7)N(1)15N(2)O(3) 0.0 Isotopic label 2 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 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)C(=O)O)=O)=O)=O)CCC1)C 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