Run Your First Analysis

A complete walkthrough from opening LEAF to seeing your first peak — about 5 minutes.

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

What you need

Two files:

1. One folder of Thermo .raw files — your LC-MS samples. Even a single file is enough for this walkthrough.
2. One CSV listing the metabolites you want to find — see below.

Make a metabolite CSV

Open a text editor and save this 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 the retention times to match your method. Don't worry about getting them exactly right — LEAF tolerates some drift. See Prepare your data for the full CSV format.

Step 1: Pick your RAW folder

On the Extract page, click Select Folder and choose the folder with your .raw files. The number of files appears next to the folder name.

[Screenshot: folder selector with files counted]

Step 2: Drop your CSV

Drag compounds.csv onto the upload zone — or click to browse. You'll see your compounds parsed into a table. Click Validate to check for formula or adduct errors.

[Screenshot: compound list editor with validated rows]

Step 3: Set parameters

For your first run, leave the defaults — they're sensible for most experiments:

Setting	Default	What it means
Polarity	NEG	Match your LC-MS method's polarity
Mass tolerance	5 ppm	How tightly to match m/z values
RT window	0.5 min	How far from expected RT to search
Peak picking	On (v4 Advanced)	Detect peak boundaries automatically
Quality scoring	On	Flag unreliable compounds

If your method ran in positive mode, switch Polarity to POS. That's usually the only setting that needs changing for a first run.

Step 4: Start

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

[Screenshot: floating action button showing job in progress]

Wait for the spinner to turn into a green checkmark. For a single RAW file with 5 compounds, this takes a few seconds. For a 50-file dataset with 200 compounds, expect a couple of minutes.

Step 5: See your results

When done, click the green checkmark, then Open in the jobs panel. LEAF opens the Peak Picking view with your data loaded.

[Screenshot: Peak Picking view with one metabolite selected]

Click any metabolite in the left-hand list. You'll see:

• EIC chart (top right) — the chromatogram for that metabolite across every sample
• Isotopologue bars (bottom left) — peak intensity per isotope (M+0, M+1, ...)
• Quality info (bottom right) — the verdict (good / warning / poor) with reasons

That's it. You ran an extraction, picked peaks, scored them, and visualized the results.

What to do next

• Group your samples — click the lightning-bolt icon in the sidebar to auto-group by sample name prefix (e.g., WT_rep1, WT_rep2 → group "WT"). See Analyze.
• Visualize — open the Visualize dropdown for PCA, heatmap, volcano plot, and more. See Visualize.
• Export — click the download button to save a .msd bundle (everything) or a .csv (intensity matrix). See Export.
• Trace isotopes — for ¹³C labeling experiments, see Isotope tracing.

If something went wrong

→ Troubleshooting