Update NEWS.md file

[tonywu1999]

Motivation and Context

This PR updates the NEWS.md changelog file to document new features and improvements in MSstatsConvert version 1.22.0. The changes enable protein turnover workflows and enhance data quality assessment capabilities across DIA-NN and Spectronaut converters, as well as improve mass spectrometry quantification options.

Changes

Protein Turnover Support

• DIA-NN: Added labeledAminoAcids parameter to DIANNtoMSstatsFormat to enable SILAC-based protein turnover workflows, automatically distinguishing heavy and light peptide forms and populating the IsotopeLabelType column required by MSstats
• Spectronaut: Added heavyLabels parameter to SpectronauttoMSstatsFormat to classify peptides as heavy, light, or unlabeled in protein turnover experiments
• Spectronaut: Introduced peptideSequenceColumn parameter to specify which column contains peptide sequences, particularly useful for protein turnover reports with different column layouts
• Spectronaut: Automatic handling of protein turnover reports lacking fragment-level columns (e.g., FFrgLossType, FFrgIon) without requiring manual pre-processing
• Fraction Selection: Updated algorithm to prioritize light-channel coverage when selecting fractions for heavy/light isotope channels, with ties broken by highest mean intensity

DIA-NN Quality Control

• Anomaly Detection: Added calculateAnomalyScores parameter to enable automated isolation-forest based anomaly detection at the precursor level, with configurable model features via anomalyModelFeatures and optional temporal drift detection via runOrder

Spectronaut MS1 Quantification

• Intensity Column Options: Extended intensity argument in SpectronauttoMSstatsFormat to accept raw Spectronaut column names (e.g., "FG.MS1Quantity") in addition to existing options like "PeakArea" and "NormalizedPeakArea"

Unit Tests

No unit tests were added or modified in this documentation-only change.

Coding Guidelines

Not applicable — this PR contains only documentation updates to the NEWS.md changelog file.

[coderabbitai]

📝 Walkthrough

Walkthrough

The NEWS.md changelog documents new features in MSstatsConvert 1.22.0, including protein turnover workflow support through DIA-NN and Spectronaut converters, anomaly scoring capabilities for DIA-NN, enhanced parameter handling for isotope labeling and peptide sequence selection, and improved MS1 quantification flexibility.

Changes

Cohort / File(s)	Summary
Changelog Documentation NEWS.md	Added changelog entries documenting new MSstatsConvert 1.22.0 features: DIA-NN labeledAminoAcids and anomaly scoring support, Spectronaut heavyLabels and peptideSequenceColumn parameters, protein turnover workflow enhancements, fraction selection logic improvements, and expanded MS1 intensity argument flexibility.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Possibly related PRs

• original implementation of spectronaut converter updates #122 — Implements the Spectronaut/DIA-NN feature additions (peptideSequenceColumn, heavyLabels, FG.MS1Quantity handling) that are documented in this NEWS entry.
• Diann turnover #128 — Implements protein turnover conversion logic (labeledAminoAcids, isotope-label classification) for DIANN/Spectronaut that corresponds to the documented features.
• Feature diann anomaly #119 — Implements DIA-NN anomaly-scoring functionality (calculateAnomalyScores, anomalyModelFeatures parameters) documented in this changelog.

Suggested reviewers

• mstaniak

Poem

🐰 The changelog hops with joy so bright,
New turnover features, isotopes in flight!
Anomaly scores and labels galore,
Version 1.22.0 opens every door! 🌟

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'Update NEWS.md file' is vague and generic, lacking specificity about what NEWS.md changes were made.	Use a more descriptive title that specifies the key features added, such as 'Add support for protein turnover workflows and anomaly scoring in MSstatsConvert 1.22.0'.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description check	✅ Passed	The pull request provides a comprehensive and well-structured description that exceeds template requirements, detailing specific features, parameters, and improvements across multiple converter modules.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch news

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