feat: add lactyl and formyl modifications with SMILES#384
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- Add Lactyl@K, Lactyl@Any_N-term, Lactyl@Protein_N-term modifications - Add SMILES for Formyl@K, Formyl@Any_N-term, Formyl@Protein_N-term - Add msfragger mappings for lactyl and formyl modifications - Add dimethyl modifications to msfragger default mod list 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
- Add YnLactyl@K, YnLactyl@Any_N-term, YnLactyl@Protein_N-term (click chemistry probe) - Fix Lactyl SMILES to use correct L-lactic acid stereochemistry ([C@@h]) - Add msfragger mappings for YnLactyl 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
When multiple modifications have similar masses within tolerance, return the one with the closest mass match instead of the first one. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Remove dead code branch for X/Any mod sites and reduce nesting with early continue. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
GeorgWa
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mschwoer
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Pull request overview
This PR adds support for lactyl and formyl post-translational modifications, along with their SMILES representations, to enable their detection and analysis in mass spectrometry data.
- Adds Lactyl and YnLactyl modifications for K, Any_N-term, and Protein_N-term sites with SMILES structures
- Adds SMILES representations for existing Formyl modifications (K, Any_N-term, Protein_N-term)
- Updates MSFragger modification mappings and default mass-mapped modification list to include lactyl, formyl, and dimethyl variants
- Refactors mass matching logic to select the closest mass match when multiple modifications fall within tolerance
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| alphabase/constants/const_files/modification.tsv | Adds SMILES structures for Lactyl, YnLactyl, and Formyl modifications at K and N-terminal positions |
| alphabase/constants/const_files/psm_reader.yaml | Adds MSFragger modification mappings for Lactyl, YnLactyl, and Formyl, and expands default mass-mapped modifications list |
| alphabase/psm_reader/msfragger_reader.py | Refactors _match_mod_by_mass to find closest mass match instead of first match within tolerance |
| tests/unit/psm_reader/test_msfragger_modification_translation.py | Adds test coverage for closest mass matching behavior with Formyl and Dimethyl modifications |
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Author
|
I had to fix a bug where any modification was matched by mass and not the closest |
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
lucas-diedrich
approved these changes
Jan 5, 2026
Collaborator
Author
|
This is really annoying, It cant be expected, that the reviewer has to compare the masses. I will write a test for this. |
Add test to verify all MSFragger modification masses in psm_reader.yaml are truncated (not rounded) to exactly 4 decimal places. Fixed masses: - Dimethyl:2H(6)13C(2)@K/Any_N-term: 36.0757 -> 36.0756 - YnLactyl@K/Any_N-term: 239.1270 -> 239.1269 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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Summary
Stacked on #380 (add-dimethyl)
🤖 Generated with Claude Code