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Optimization

In the Optimization tab, the EICs are computed first based on the parameters defined in the Targets table. Next, target RT windows (rt_min, rt_max) can be refined so downstream extraction in Processing captures the correct peak region.

Optimization

Tip: Click the help icon (small "i" symbol) next to the "Optimization" title to take a guided tour of this section.

Peak Optimization Workflow

  1. Compute Chromatograms: Click COMPUTE CHROMATOGRAMS to generate EIC traces.
  2. Preview Cards: Inspect chromatogram previews per target.
  3. Open Manual View: Click a card (or graph icon) to fine-tune RT ranges.
  4. Persist Changes: Auto-save events.

1. Compute Chromatograms

COMPUTE CHROMATOGRAMS opens a modal to configure recomputation and resources.

  • MINT validates prerequisites first (requires at least one optimization sample and one target).
  • If chromatograms already exist, MINT shows a warning and enables recompute toggles (MS1, MS2) automatically.
  • Default resources are auto-detected from your system (CPU/RAM), and batch size is auto-calculated from workload and resource settings.
  • If no targets are selected, MINT computes chromatograms for all targets.
  • After chromatograms are generated, MINT runs adaptive RT-span optimization for targets marked as auto-adjusted during import.

2. Preview Cards

After computation, Optimization cards provide a quick glance at the data before manual edits.

Optimization

  • Card Plot: per-target chromatogram view over the current RT span.
  • Bookmark toggle: star targets for later focused processing.
  • Delete target: remove target plus related chromatogram/results entries.
  • Pagination and sizing: browse with pagination and tune card width/height for your screen.
Preview filters
  • Filter by ms_type (all, ms1, ms2).
  • Filter by bookmark state (all, Bookmarked, Unmarked).
  • Order cards by peak label or m/z.
  • Toggle log-y rendering for quick visual contrast checks.

3. Interactive Manual Optimization

Open a target card to launch the detailed modal and adjust RT spans directly on the plot. Move across targets without closing the modal. Changes are saved automatically.

Optimization

  • Edit RT-span: drag/resize the RT window when unlocked.
  • Lock range: prevent accidental RT-window edits.
  • Set RT marker: click within the span to set/update target RT.
  • Scale and grouping: switch linear/log y-axis and group-click legend behavior.
  • Notes: edit target notes while inspecting traces.
Advanced modal controls
  • Megatrace: aggregated rendering mode for large trace sets.
  • Full range: show full chromatogram instead of local window (can be slower).
  • RT Alignment: align traces by apex within current RT span; alignment state is persisted per target.

4. Auto-save and persistence

MINT includes persistence and consistency behaviors so optimization work is resilient:

  • On target navigation (Prev/Next), changed RT span and RT-alignment state are auto-saved.
  • On modal close, changed RT span / RT alignment are auto-saved.
  • Notes are persisted in navigation flows.
  • Use Save when you want immediate explicit commit feedback while staying on the same target.

Card Controls

  • Bookmarking a target also marks it as selected (peak_selection = TRUE).
  • This keeps bookmarked subsets compatible with Processing filters such as Bookmarked Targets Only.
  • At the bottom-left of the Optimization page, adjust card Width and Height to trade off overview density vs detail visibility.