Run a First Targeted Analysis

This walkthrough starts LEAF, processes a small targeted LC-MS dataset, and opens the processed result for chromatogram review. The procedure takes approximately 5 minutes with a small input folder.

[Screenshot: full LEAF window showing the Extract view, ready to start]

Prerequisites

LEAF should already be installed by one of the supported local paths:

• Install the wheel + CLI — launches the local server and opens it in a browser.

Hosted MINT access is under development and not yet available for general use.

For a local install, launch LEAF in a terminal:

Standalone installer (Path A)

~/.leaf/leaf
# Open http://127.0.0.1:8000

Manual wheel + CLI (Path B)

leaf webui run
# Open http://127.0.0.1:18008

The browser opens on the Extract view.

Inputs

Two inputs are required:

1. A folder of LC-MS files — Thermo .raw or .mzml (.mzml.gz is also accepted). A single file is sufficient for this walkthrough.
2. A CSV listing the target metabolites — described below.

Create a metabolite CSV

The recommended command-line setup is:

leaf init ./leaf-run

This creates leaf-run/metabolites.csv, plus empty raw/ and results/ folders. Place the LC-MS files in leaf-run/raw/, then use the generated CSV as the starting list.

The release also includes examples/metabolite-list-primary-metabolism.csv, a primary-metabolism panel with representative retention times.

For a minimal test, save the following as compounds.csv:

Metabolite,Formula,RetentionTime,Adduct
Glucose,C6H12O6,5.2,M-H
Lactate,C3H6O3,3.1,M-H
Citrate,C6H8O7,8.5,M-H
Pyruvate,C3H4O3,2.8,M-H
Glutamate,C5H9NO4,4.1,M-H

Adjust retention times to match the chromatographic method. Exact values are not required for this walkthrough because the RT search window allows moderate drift. See Prepare Data for the complete CSV specification.

Optional preflight:

leaf validate ./compounds.csv ./path/to/raw-folder

Step 1: Select the data folder

On the Extract page, click Select Folder and choose the folder containing .raw, .mzml, or .mzml.gz files. LEAF displays the file count next to the folder name.

[Screenshot: folder selector with files counted]

Step 2: Load the compound list

Drag compounds.csv onto the upload zone, or click to browse. LEAF parses the compounds into an editable table. Click Validate to check formulas, adducts, retention times, and duplicate entries.

[Screenshot: compound list editor with validated rows]

Step 3: Set parameters

For an initial run, the default parameters are appropriate for many targeted LC-MS methods:

Setting	Default	What it means
Polarity	AUTO	Resolves to NEG for targeted runs unless POS is selected
Mass tolerance	5 ppm	How tightly to match m/z values
RT window	0.4 min	How far from expected RT to search
Peak picking	On	Detect peak boundaries automatically
Quality scoring	On	Flag unreliable compounds

If the acquisition was performed in positive mode, change Polarity to POS. This is typically the only parameter requiring adjustment for a first run.

Step 4: Start

Click Start Processing. A floating progress button appears in the bottom-right corner.

[Screenshot: floating action button showing job in progress]

Processing is complete when the spinner changes to a green checkmark. Runtime depends on file size, reader backend, storage speed, and compound count. A single input file with a small compound list generally completes within a short interval; larger batches may take several minutes.

Step 5: Review results

After completion, click the green checkmark, then Open in the jobs panel. LEAF opens the Peak Picking view with the processed dataset loaded.

[Screenshot: Peak Picking view with one metabolite selected]

Click any metabolite in the left-hand list. The linked panels show:

• EIC chart (top right) — chromatograms for the selected metabolite across samples
• Isotopologue bars (bottom left) — peak intensity per isotopologue when tracing is configured
• Quality info (bottom right) — the compound-level verdict and supporting warnings

The walkthrough has covered targeted extraction, peak picking, quality scoring, and result inspection.

Further steps

• Sample grouping — click the lightning-bolt icon in the sidebar to group samples by name prefix (e.g., WT_rep1, WT_rep2 → group "WT"). See Analyze.
• Visualization — open the Visualize dropdown for PCA, heatmaps, volcano plots, and additional chart types. See Visualize.
• Export — click the download button to save a .msd archive (full bundle) or a .csv (intensity matrix). See Export.
• Isotope tracing — for ¹³C and other labeling experiments, see Isotope tracing.

Troubleshooting

→ Common issues and resolutions