[FEATURE] Temporal QC degradation assessment and alerts for QC metric thresholds

[ypriverol]

Feature Description

Would be great to have in pmultiqc some kind of alert and assesments for the QC metrics, including medians and defined thresholds:

• Visual assessment for temporal degradation in MS data quality (e.g., detecting drift, instrument issues, or performance drops across large/longitudinal studies).
• Built-in guidance/alerts when important QC metrics fall below user-defined or reference thresholds.

These features will assist users in quickly understanding time-based trends and quality failures, especially in big or ongoing proteomics projects, and make automated QC more actionable for both experienced and new users.

Use Case

• Large/longitudinal proteomics studies where instrument or sample quality may change over time.
• New users or sites where actionable threshold-based guidance helps prevent misinterpretation.
• Routine QC monitoring where staff need to be alerted about drift or drops in main scores.

Feature Details

• Temporal Degradation Visualization: Add plots for key QC metrics (rate of IDs, MS1 signal, sequence coverage, etc.) over run/acquisition order or acquisition date, highlighting drift, step-changes, or patterns that may indicate gradual instrument decline or abrupt failures.
• Threshold Alerts: Support user- or community-defined reference thresholds for main QC metrics (e.g., missed cleavages, ID rates, intensity, etc.), and visually flag or annotate results that fall below these.
• Guidance in Reports: Add brief, contextual guidance for interpreting flagged or out-of-range metrics directly in the HTML reports (e.g., via notes or tooltips), with the option to customize or auto-generate using LLMs.
• Configurable: All methods should be CLI/YAML/UI configurable, with clear defaults and documentation. Heavy/facility users can tune as needed.
• Documentation: Examples, use cases, and recommended threshold tables in user docs and output.

Expected Interface/Experience

• Trend/line plots or heatmaps for selected metrics, per sample or time, with clear annotation of drifts/shifts.
• QC reports visually highlight (color, icons, notes) samples/runs outside thresholds, optionally with interpretive notes.
• Users can provide YAML/CLI definitions for metric thresholds and toggle guidance/alert features.
• Documentation clearly describes features and configuration.

Priority

Medium - Would be helpful

Additional Context

• Implements suggestions from Reviewer 3 of the pmultiqc JPR paper.
• Reference tools: MSstatsQC, common QC/QA guidance in proteomics.
• See also: Large dataset/report scalability, FragPipe/MSFragger support.

Code of Conduct

• I agree to follow this project's Code of Conduct