Analyze Results

After extraction completes, the Peak Picking view is where you inspect each compound, check peak quality, and adjust integrations. This is the page you'll spend the most time on.

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

Open the view

Two ways to get here:

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 plus four central panels:

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

Sample selector (left sidebar)

Lists every sample in your 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 Area Top (intensity at peak apex) and Area Sum (total area under curve)

[Screenshot: sample selector with grouping applied]

Metabolite table (top-left panel)

A scrollable list of every compound in your dataset. Click any row to load 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 interactive chromatogram for the selected metabolite, overlaying every selected sample.

• Colored traces — individual samples (gradient from cyan to purple, or by group color when grouping is on)
• Red dashed line — expected retention time from your 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.

Verdict criteria

Criterion	Good	Warning	Poor
Detection rate	≥ 20%	—	< 20%
RT deviation	—	—	> 0.8 min
Peak shape score	≥ 0.70	—	< 0.50
RT clusters	1 group	≥ 2 groups with spread > 0.1 min	—
Multi-peak samples	—	> 40 samples	—

Mark compounds for export

The verdict filter also drives export. If you want only the green compounds in your CSV/.msd, filter to Good before downloading. See Export.

Next step

→ Visualize statistically