fix(turnover): Fix DIANN 1.8 processing of protein turnover labeling#140
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📝 WalkthroughWalkthroughIsotope-label suffix parsing in DIANN ModifiedSequence handling now accepts any non-dash label token before the amino-acid H/L suffix. Regexes, warnings, tests, and documentation are updated, and internal ProteinProspector documentation is generated. ChangesGeneric isotope-label suffix parsing
ProteinProspector documentation
Estimated code review effort: 2 (Simple) | ~10 minutes Possibly related PRs
Suggested reviewers: Poem
🚥 Pre-merge checks | ✅ 5✅ Passed checks (5 passed)
✨ Finishing Touches🧪 Generate unit tests (beta)
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🧹 Nitpick comments (1)
R/clean_DIANN.R (1)
268-276: 📐 Maintainability & Code Quality | 🔵 Trivial | ⚡ Quick winConsider consolidating the three regex constructions.
heavy_regex,light_regex, andstrip_regexrepeat the same\\([^-]+-(?:aa_pattern)-...scaffold with only the trailing suffix differing. A single pattern with a capture group (e.g. matching-([HL])\)) could drive both classification and stripping, reducing the chance of the three patterns drifting out of sync during future edits.♻️ Possible consolidation
- heavy_regex <- paste0("\\([^-]+-(?:", aa_pattern, ")-H\\)") - light_regex <- paste0("\\([^-]+-(?:", aa_pattern, ")-L\\)") - strip_regex <- paste0("\\([^-]+-(?:", aa_pattern, ")-[HL]\\)") + label_regex <- paste0("\\([^-]+-(?:", aa_pattern, ")-([HL])\\)") + heavy_regex <- paste0("\\([^-]+-(?:", aa_pattern, ")-H\\)") + light_regex <- paste0("\\([^-]+-(?:", aa_pattern, ")-L\\)") + strip_regex <- label_regex🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@R/clean_DIANN.R` around lines 268 - 276, The three regex variables in clean_DIANN reuse the same scaffold and should be consolidated to avoid drift. Update the regex construction near .classifyIsotopeLabelType so a single shared pattern (with a capture for the H/L suffix) can be used to derive heavy_regex, light_regex, and strip_regex consistently, while keeping the current behavior in dn_input and PeptideSequence stripping.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Nitpick comments:
In `@R/clean_DIANN.R`:
- Around line 268-276: The three regex variables in clean_DIANN reuse the same
scaffold and should be consolidated to avoid drift. Update the regex
construction near .classifyIsotopeLabelType so a single shared pattern (with a
capture for the H/L suffix) can be used to derive heavy_regex, light_regex, and
strip_regex consistently, while keeping the current behavior in dn_input and
PeptideSequence stripping.
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: dfd2c1d6-44a4-4b94-b81f-368001b9392e
📒 Files selected for processing (6)
R/clean_DIANN.RR/converters_DIANNtoMSstatsFormat.Rinst/tinytest/test_clean_DIANN.Rman/DIANNtoMSstatsFormat.Rdman/MSstatsClean.Rdman/dot-cleanRawDIANN.Rd
1 participant
Motivation and context
DIANN 1.8 turnover labeling in MSstatsConvert was not handling
ModifiedSequencelabels flexibly enough. The fix generalizes isotope-label parsing so turnover/labeled peptides can be recognized even when the label token is not literallySILAC.Summary of solution
The DIANN parsing logic was updated to detect generic label suffixes of the form
(<label>-<AA>-H/L)and to strip them from peptide sequences while assigning the correct isotope label type.Detailed changes
.assignDIANNIsotopeLabelType()to support generic label tokens instead of onlySILAC.ModifiedSequenceparsing regexes to match:(<label>-<AA>-H)(<label>-<AA>-L)where
<label>is any non-dash token and<AA>is restricted to the configured labeled amino acids.SILAC-K-H/L(label-K-H/L)verifying correct
IsotopeLabelTypeassignment and peptide stripping.Tests
inst/tinytest/test_clean_DIANN.Rfor generalizedModifiedSequencelabel parsing.Coding guidelines
Motivation and Context
DIANN 1.8 can encode protein-turnover labels in
ModifiedSequenceusing label tokens beyondSILAC. Previously, MSstatsConvert recognized only SILAC-specific suffixes, preventing correct classification of generic labels.The parser now supports
(<label>-<AA>-H/L)suffixes with configured labeled amino acids, strips recognized annotations, and preserves existing channel-based DIANN behavior.Changes
SILAC-K-H/Llabel-K-H/L.cleanRawProteinProspector.Unit Tests
.assignDIANNIsotopeLabelTypetests to verify:H/Lclassification.NAfor unlabeled peptides.PeptideSequence.Coding Guidelines