leaf targeted

Headless targeted extraction runs the same processing path as the Extract page without opening a browser. It writes a result CSV and, by default, a .msd archive for reopening in LEAF.

Synopsis

leaf targeted INPUT_PATH COMPOUND_LIST OUTPUT_DIR [OPTIONS]

Required arguments

Argument	Description
INPUT_PATH	A single .raw, .mzml, or .mzml.gz file, or a folder containing one supported format
COMPOUND_LIST	Path to the metabolite CSV (see Prepare Data for the schema)
OUTPUT_DIR	Directory where LEAF writes result files

Common flags

Flag	Default	Description
--polarity {NEG,POS}	NEG	MS polarity for mass calculation. Must match the acquisition.
--tolerance INT	5	m/z tolerance in ppm for EIC extraction.
--rt-window FLOAT	0.3	Retention-time search window in minutes.
--backend {auto,rust,dotnet}	auto	Input-file reader. rust uses SEED; dotnet uses Thermo's RawFileReader for .raw files.
--parallel / --no-parallel	off	Use the .NET parallel extraction path when --backend dotnet is selected.
--max-workers INT	4	Parallel extraction threads.
--skip-blank / --no-skip-blank	on	Skip files whose name contains "blank".
--organize-name / --no-organize-name	on	Auto-parse clean sample names from file names.
--tracing-path PATH	(none)	Path to a JSON tracing config (export from the web UI's Tracing Editor). See Isotope tracing.
--correct / --no-correct	off	Apply natural-abundance isotope correction after scoring.
--tracer ELEMENT:PURITY	(none)	Tracer element and purity for correction, repeatable. Example: --tracer 13C:0.99. Current correction allowlist: C, H, N.
--high-res / --low-res	high-res	High-resolution correction mode. Low-resolution mode is rejected in the current correction path.
--extract-ms2 / --no-extract-ms2	on	Extract MS² spectra when present. MS² extraction uses the SEED backend.
--save-extract / --no-save-extract	on	Write the extracted .msd bundle.

For the full flag set, run leaf targeted --help.

Recipe — minimal targeted run

leaf targeted ./samples ./compounds.csv ./outputs --polarity NEG --tolerance 5

Writes a result CSV and .msd archive into ./outputs. Use --no-save-extract only when the archive is not required.

Recipe — tracing run

leaf targeted ./samples ./compounds.csv ./outputs \
  --polarity NEG --tolerance 5 \
  --tracing-path ./tracing-13C.json \
  --save-extract

The tracing JSON is produced by the web UI's Tracing Editor (Export button) or hand-written — see Isotope tracing.

Recipe — natural-abundance corrected tracing output

leaf targeted ./samples ./compounds.csv ./outputs \
  --polarity NEG --tolerance 5 \
  --tracing-path ./tracing-13C.json \
  --correct --tracer 13C:0.99 \
  --save-extract

This writes the standard result CSV plus a corrected CSV. When correction is enabled, LEAF also saves an .msd archive carrying the tracer configuration.

Recipe — overriding the backend

# Force the Thermo .NET reader on Windows when SEED cannot decode a file:
leaf targeted ./samples ./compounds.csv ./outputs --backend dotnet

Hidden alias

leaf analyze is a hidden alias for leaf targeted. New scripts should use the canonical name.

Next

→ Configuration — backend selection on disk