Analyze Results

After extraction completes, the Peak Picking view is the primary interface for reviewing targeted results. It supports chromatogram inspection, sample comparison, quality-verdict review, and manual adjustment of peak regions when required.

[Screenshot: full Peak Picking view with a metabolite selected]

Open the view

Opening methods:

1. After an extraction finishes, click Open in the jobs panel
2. From any page, drag a previously-saved .msd file onto the window

Layout

The view has a left sidebar and four central panels:

┌─────────────┬───────────────────────────────────┐
│ Sample      │  Metabolite Table  │  EIC Chart  │
│ Selector    ├───────────────────────────────────┤
│ (sidebar)   │  Isotopologues     │  Quality    │
└─────────────┴───────────────────────────────────┘

Sample selector (left sidebar)

Lists every sample in the loaded dataset.

• Checkboxes — toggle which samples appear on the charts
• Lightning-bolt button — auto-group samples by name prefix (e.g., WT_rep1, WT_rep2 → group WT)
• Pick mode toggle — switch between apex intensity and integrated peak area

[Screenshot: sample selector with grouping applied]

Metabolite table (top-left panel)

A scrollable list of every compound in the loaded dataset. Selecting a row loads that metabolite into the EIC chart, isotopologue bars, and quality info.

Columns include:

• Verdict badge (green / orange / red)
• Compound name
• m/z (observed)
• RT (median)
• Detection rate (% of samples)

Sort by clicking a column header. Filter by verdict using the dropdown at the top.

EIC chart (top-right panel)

The EIC chart displays the selected metabolite across the selected samples.

• Colored traces — individual samples, or group-colored traces when grouping is enabled
• Red dashed line — expected retention time from the compound CSV
• Red X markers — auto-detected peaks
• Drag to select an RT range to manually define a peak region and see the recalculated areas

Adjacent RT Check tab shows retention-time deviation analysis:

• Scatter plot of manual vs. auto-detected RT values
• Summary cards: total compounds, outlier %, R² correlation, mean RT shift
• Sortable outlier table — click a row to jump to that metabolite's EIC

[Screenshot: EIC chart with multiple sample traces and detected peak markers]

Isotopologue bars (bottom-left panel)

Shows the isotope distribution (M+0, M+1, M+2, ...) for the selected metabolite.

• Toggle grouped vs stacked bar mode
• Toggle absolute intensity vs percentage display
• When grouping is on, bars show mean ± SEM per group
• Color-coded: M+0 (blue), M+1 (green), M+2 (amber), M+3 (rose), ...

For tracing experiments, switch to Percentage mode to see fractional labeling — useful for comparing labeling between conditions (e.g., WT vs KO).

→ More on isotope tracing

Quality info (bottom-right panel)

The verdict and warnings for the selected metabolite.

Verdict	Color	Meaning	Action
Good	Green	Reliable peak with consistent shape and detection	Use in analysis
Warning	Orange	Usable but has caveats (co-elution, multiple peaks)	Review manually
Poor	Red	Unreliable (low detection, wrong RT, poor peak shape)	Exclude or investigate

Warnings are listed below the verdict with severity badges (CRITICAL, WARNING, MINOR, INFO) and per-sample detail.

The scoring model is intended as a review aid rather than an automatic exclusion rule. Record manual review decisions when a compound is biologically important or when the chromatogram indicates a known method-specific behavior.

Mark compounds for export

The verdict filter also affects export. Filter to Good before downloading when the downstream analysis should contain only compounds that passed review. See Export.

Also from a script

Re-running peak picking on an existing .msd from Python:

from leaf.analyzer import Samples, PeakPicking
samples = Samples.load("analysis.msd")
PeakPicking(samples).run()
samples.save("analysis.msd")

→ Python recipes

Next step

→ Visualize statistically