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Add support for N-terminal ubiquitination (diglycine remnant on protein N-terminus), a non-canonical modification catalyzed by UBE2W. - Add GlyGly@Any_N-term to modification.tsv with SMILES - Add msfragger modification mapping for mass-based recognition - Add to mass_mapped_mods list for msfragger_psm_tsv reader 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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What is the real mass decimal place (e.g. N-term(114.0429)) of MSFragger modification? |
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As far as I know, MSFragger uses 4 decimal places without rounding (just cutoff). |
GeorgWa
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Pull request overview
This PR adds support for N-terminal ubiquitination by introducing the GlyGly@Any_N-term modification. This represents a non-canonical modification catalyzed by UBE2W, which differs from the more common K-linked ubiquitination.
- Adds the
GlyGly@Any_N-termmodification entry to the modification database - Configures MSFragger mass-based recognition via
N-term(114.0429)mapping - Enables the modification for MSFragger PSM TSV reader
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| alphabase/constants/const_files/modification.tsv | Adds the new GlyGly@Any_N-term modification entry with SMILES structure and chemical composition |
| alphabase/constants/const_files/psm_reader.yaml | Adds MSFragger mapping and includes the modification in the mass_mapped_mods list |
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Mass 34.068961 should be truncated to 34.0689, not rounded to 34.0690. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
This reverts commit 8234e08.
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- Add GG@Any_N-term to modification.tsv - Remove duplicate GlyGly@K and GlyGly@Any_N-term entries - Update psm_reader.yaml to use GG@ instead of GlyGly@ - Update sage_reader notebook test 🤖 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>
Use same SMILES pattern as GG@Any_N-term with [Ts] placeholder. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
GeorgWa
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Pull request overview
Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.
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| GG@Protein_N-term 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Post-translational 121 NCC(=O)NCC(=O)[Ts] 0.0 | ||
| GG@Any_N-term 114.042927 114.1026 H(6)C(4)N(2)O(2) 0.0 Multiple 121 NCC(=O)NCC(=O)[Ts] 0.0 |
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The SMILES strings for GG@Protein_N-term and GG@Any_N-term are identical (NCC(=O)NCC(=O)[Ts]), but they have different classification categories (Post-translational vs Multiple). Consider documenting why these modifications have the same chemical structure but different categories, or if they should have distinct SMILES to reflect their different biological contexts.
Update references to use consistent GG@K naming after removing GlyGly@K duplicate from modification.tsv. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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Could you rerun the notebook? Otherwise the respective outputs will not be shown in the readthedocs documentation
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Could you rerun this notebook as well?
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🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
could this be documented explicitly somewhere, e.g. in the yaml file @GeorgWa ? |
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