Prepare Your Data

Before you launch an analysis, you need two things in front of you: your RAW files and a metabolite list.

RAW files

LEAF reads Thermo Fisher .raw files directly. Put all the files for one experiment into a single folder. LEAF will process every .raw file in the folder.

Naming: name your files descriptively — e.g., WT_rep1.raw, WT_rep2.raw, KO_rep1.raw. LEAF can auto-extract clean sample names from the file name and auto-group replicates by name prefix.

Blanks: include them in the folder if you want — LEAF skips files with "blank" in the name by default.

Metabolite list (CSV)

A CSV listing the compounds you want to quantify.

Required columns

Column	Description	Example
Metabolite	Compound name (also accepts Compound or Name)	Glucose
Formula	Molecular formula	C6H12O6
RetentionTime	Expected retention time in minutes (also accepts RT)	5.2
Adduct	Ionization adduct	M-H

Optional columns

Column	Description
Mass	Exact m/z value. If omitted, LEAF calculates it from formula + adduct.
Pathway	Pathway annotation, used for pathway-network visualizations.
Notes	Free-text notes shown in the compound editor.

Flexible naming

LEAF recognizes common column-name variants:

• Metabolite / Compound / Name
• Formula / MolecularFormula
• RetentionTime / RT / retention_time
• Adduct / IonizationAdduct

Example

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
Succinate,C4H6O4,7.2,M-H
Malate,C4H6O5,6.5,M-H
Fumarate,C4H4O4,7.0,M-H

A starter list for primary metabolism is included with LEAF — see examples/metabolite-list-primary-metabolism.csv in the repository.

For untargeted analysis

You don't need a metabolite CSV for untargeted runs. LEAF discovers features automatically from your RAW files. See Untargeted analysis.

For isotope tracing

Use the same CSV — no extra columns needed. Isotopologues (M+1, M+2, ...) are configured in the Tracing Editor on the Extract page, not in the CSV. See Isotope tracing.

Validating before you launch

After uploading the CSV, click Validate in the compound list editor. LEAF flags:

• Missing required columns
• Invalid molecular formulas (typos, unsupported elements)
• Unrecognized adducts
• Duplicate compound names

Fix the warnings before you start the extraction.

[Screenshot: compound list editor showing validation warnings]

Next step

→ Extract