feat: add PSMtag light modification for K and N-term#388
Merged
Conversation
Add PSMtag (photocleavable mass tag) modifications: - PSMtag@K: lysine epsilon-amine conjugation - PSMtag@Any_N-term: N-terminal conjugation - Add msfragger modification mapping K(308.1160), N-term(308.1160) - Add to mass_mapped_mods for msfragger_psm_tsv Delta mass: 308.116092 Da, Formula: C(18)H(16)N(2)O(3) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
GeorgWa
requested review from
Copilot,
lucas-diedrich and
mschwoer
and removed request for
Copilot and
lucas-diedrich
There was a problem hiding this comment.
Pull request overview
This PR adds support for PSMtag light modification, a photocleavable mass tag used for proteomics analysis. The modifications are defined for lysine residues and N-terminal positions with a delta mass of 308.116092 Da.
Key changes:
- Added PSMtag modification definitions for K and Any_N-term sites
- Configured MSFragger reader to recognize PSMtag modifications
- Added modification mappings for PSMtag variants
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| alphabase/constants/const_files/psm_reader.yaml | Added PSMtag modification mappings and MSFragger mass-mapped modifications |
| alphabase/constants/const_files/modification.tsv | Added PSMtag modification definitions with mass, formula, and SMILES notation |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Resolve conflicts in modification.tsv and psm_reader.yaml by keeping both PSMtag modifications from add-psm-tag and Lactyl/YnLactyl/Dimethyl modifications from main. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
PSMtag@K: lysine epsilon-amine conjugationPSMtag@Any_N-term: N-terminal conjugation🤖 Generated with Claude Code