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Pull request overview
This PR adds SMILES structure support for TMT 10plex and TMTpro modifications to enable full chemical structure representation of these isotopic labels.
- Adds SMILES notation to TMT10plex@Any_N-term and TMT10plex@K modifications
- Adds SMILES notation to TMTpro@Any_N-term and TMTpro@K modifications
- Adds TMTpro modification mappings to the PSM reader configuration
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| alphabase/constants/const_files/modification.tsv | Adds SMILES structures to TMT10plex and TMTpro modifications, populating previously empty structure fields |
| alphabase/constants/const_files/psm_reader.yaml | Adds TMTpro@K and TMTpro@Any_N-term modification mappings for PSM reader |
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| 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 |
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The modification name 'TMT10plex' is inconsistent with the existing 'TMT6plex' naming pattern. Based on the PR title mentioning 'TMT 10plex', this should likely be 'TMT10plex' throughout, but verify this matches the expected naming convention for 10-plex TMT modifications in the codebase.
| 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)C(=O)O)=O)=O)=O)CCC1)C 0.0 |
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The SMILES structures added for TMT10plex@K and TMTpro@K contain embedded lysine residues (NCCCCC@HC(=O)O). Verify these represent the modification attachment to lysine correctly, as including the full amino acid in the SMILES may cause issues with mass calculations or structure interpretation depending on how these are processed downstream.
| 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 C(=O)CCCNC(=O)CCCNC(=O)C1N(CC(C)C)CCC1 0.0 |
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Checked masses, IDs + composition based on unimod reference: https://www.unimod.org/modifications_view.php?editid1=737
a) Is the smiles string for the TMT10plex@Any_N-term modification correct?
b) Would it make sense to add the smiles strings to the other entries as well?
| 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 |
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Using this product sheet as reference, I think the smiles string is incorrect
The smiles currently evaluates to:
- Currently Pyrrolidine ring instead of Piperidine ring
- Currently 3-C tail between amide bond and terminal aldehyde instead of 2-C tail
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Suggested edit:
C1(C)CCCC(C)N1CC(=O)NCCC(=O)
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Thanks for catching this! I'm a bit confused tbh. I reviewed this quite thoroughly
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 <noreply@anthropic.com>
Adds full smiles support for tmt 10plex modifications