Extract
The Extract page is where you configure parameters and launch a processing run. This is the first step of every targeted analysis.
[Screenshot: full Extract view with parameters configured and compound list loaded]
Layout
The Extract page has four panels:
| Panel | Position | Purpose |
|---|---|---|
| Folder selector | Top-left | Choose which RAW files to process |
| Compound list editor | Center | Upload, edit, and validate your metabolite CSV |
| Parameters sidebar | Right | Polarity, mass tolerance, RT window, peak picking, scoring |
| Tracing editor | Right (below parameters) | Configure isotopologues for tracing experiments |
Select RAW files
Local mode (desktop)
Click the folder selector and choose the folder containing your .raw files. The file count appears next to the folder name.
Server mode (hosted)
Search and select folders from the list. Use the checkboxes to select multiple folders at once.
[Screenshot: folder selector in both local and server modes]
Upload your compound list
Drag and drop your CSV onto the upload zone, or click to browse. LEAF parses it and shows the compounds in an editable table.
After uploading, click Validate to check for errors. Common issues (missing formulas, invalid adducts) appear as warnings — fix them before continuing.
Set parameters
| Parameter | Recommended | Range | What it does |
|---|---|---|---|
| Polarity | Match your method | NEG / POS | Must match your LC-MS acquisition polarity |
| Mass Tolerance | 5 ppm | 1–50 ppm | EIC extraction window. Lower is stricter. Color-coded: green ≤5, yellow 5–15, red >15. |
| RT Window | 0.5 min | 0.1–5.0 min | How far from expected RT to search for peaks |
Peak picking
Toggle peak picking on (recommended). Choose a detection method:
| Method | Label | Best for |
|---|---|---|
| v4 | Advanced | Most experiments — best accuracy and peak shape detection |
| v2 | Smoothed | Noisy data — uses Savitzky-Golay smoothing |
| v1 | Basic | Quick exploratory runs |
Additional toggles:
- Organize names (on by default) — extracts clean sample names from RAW file names (e.g.,
WT_rep1_240301.raw→WT_rep1) - Skip blanks (on by default) — automatically skips files with "blank" in the name
Quality scoring
Toggle quality scoring on (recommended). LEAF assigns each compound a verdict (good / warning / poor) based on detection rate, peak shape, and RT consistency.
| Parameter | Default | What it means |
|---|---|---|
| SNR Threshold | 3 (lenient) to 20 (strict) | Signal-to-noise ratio cutoff |
| LOD Threshold | 100,000 | Minimum intensity for a peak to count as detected |
Tracing (optional)
For isotope-labeling experiments, configure the Tracing Editor before starting. See Isotope tracing.
Start processing
Once folders are selected and compounds validated, the Start Processing button turns blue. Click it.
A floating action button appears in the bottom-right corner:
| State | Meaning |
|---|---|
| Blue with spinner | Job running — shows % progress |
| Green with checkmark | Job done — click to download or open |
| Red with warning icon | Job failed — click for details |
[Screenshot: floating action button cycling through states]
Click the button to open the jobs panel with full progress, per-file status, and Download / Open options.
Untargeted instead?
The Extract page has a Targeted / Untargeted toggle at the top. Switch to Untargeted mode for feature discovery without a compound list. See Untargeted analysis.