Extract — Targeted
The Extract page configures and starts a targeted LC-MS processing run. This page documents the targeted workflow only.
[Screenshot: full Extract view with parameters configured and compound list loaded]
Layout
The Extract page has four working areas:
| Panel | Position | Purpose |
|---|---|---|
| Folder selector | Left sidebar | Choose which RAW / mzML files to process |
| Parameters sidebar | Left sidebar | Retention-time search, peak picking, grouping, scoring, backend, and file-handling options |
| Compound list editor | Center | Upload, edit, and validate the metabolite list |
| Tracing editor | Right panel | Configure isotopologues for tracing experiments |
Select files
Local mode (CLI / desktop)
Click the folder selector and choose the folder containing .raw, .mzml, or .mzml.gz files. The file count appears next to the folder name.
Server mode (MINT)
Server-mode folder browsing is reserved for the MINT integration, which is under development and not enabled for general use.
[Screenshot: folder selector in both local and server modes]
Upload the compound list
Drag and drop a CSV or TSV onto the upload zone, or click to browse. LEAF parses the file and shows the compounds in an editable table.
After uploading, click Validate to check for errors. Common issues include missing required columns, invalid formulas, invalid retention times, and duplicate compound-adduct combinations. Resolve errors before continuing.
LEAF auto-detects LEAF native (RFA), Skyline transition lists, and El-MAVEN peak tables / compound DBs based on header names.
Set parameters
Acquisition
| Parameter | Default | Range | What it does |
|---|---|---|---|
| Polarity | AUTO | AUTO / NEG / POS | Match the LC-MS acquisition polarity. In targeted runs, AUTO currently resolves to NEG when the run is submitted. |
| Mass tolerance | 5 ppm | 1–50 ppm | EIC extraction window. Lower is stricter. The slider value is color-coded: green ≤5, yellow 5–15, red >15. |
| Backend | seed (Rust) on macOS / Linux; RawFileReader (.NET) on Windows | seed / RawFileReader | Underlying RAW reader. seed is faster on Thermo files; RawFileReader is the reference implementation. Unavailable backends are disabled in the selector. |
Retention time
| Parameter | Default | Range | What it does |
|---|---|---|---|
| RT window | 0.4 min | 0.1–5.0 min | ± window around the expected RT to search for peaks |
The sidebar header summarizes the current setting, for example RT ±0.4 min.
Peak picking
Keep peak picking enabled for routine targeted analyses.
RT mode
| Mode | Behavior |
|---|---|
| Reference (default) | Use the RT from the compound list as the search center |
| Auto | Auto-detect the RT from the EIC, ignoring the compound-list value |
Use Auto when the CSV contains approximate placeholder RTs and the peak location should be inferred from the chromatograms.
Instrument settings and quality scoring
Keep quality scoring enabled for routine analyses. LEAF assigns each compound a verdict (good / warning / poor / insufficient_data) from the extracted chromatograms and configured instrument thresholds.
| Parameter | Default | What it means |
|---|---|---|
| SNR threshold | 10 | Minimum signal-to-noise ratio used during quality review. Higher values are stricter. |
| Intensity threshold | 100,000 | Peak-picking noise floor. |
| LOD (scoring) | Auto | Limit of detection used by the scoring gate. Auto derives the value from the intensity threshold. |
| Saturation flag | Auto | Intensity level that triggers a non-blocking saturation warning. |
File-handling toggles
| Toggle | Default | Effect |
|---|---|---|
| Organize names | On | Strip date/timestamp prefixes from file names for clean grouping (e.g. 20240321_WT_rep1.raw → WT_rep1). |
| Skip blanks | On | Skip files with blank (case-insensitive) in the name during extraction. |
| MS² extraction | On | Capture MS² spectra alongside MS¹ when present. This enables raw-spectrum and retention-time preview in Peak Picking. Enabling MS² automatically uses the SEED (Rust) backend. |
Tracing (optional)
For isotope-labeling experiments, configure the Tracing Editor below the parameters before starting. See Isotope tracing.
Start processing
Once the folder is selected and the compound list is valid, the Start Processing button is enabled. Click it to start the run.
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 progress, per-file status, and Download / Open options.
Also from a script
Headless equivalent of this page:
leaf targeted ./samples ./compounds.csv ./outputs \
--polarity NEG --tolerance 5 --rt-window 0.4→ leaf targeted reference Or in Python: Recipe 1 — Batch extraction