Export

When you're done analyzing, save your data so you can reopen it later or hand it off to a collaborator or downstream tool.

Two formats

Format	Use case	Contents
.msd	Reopen in LEAF, share with collaborators	Full bundle: intensities, peaks, quality scores, isotopologues, metadata, parameters
.csv	Excel, R, Python, GraphPad, etc.	Flat intensity matrix — one row per metabolite, one column per sample

How to export

Click the download button in the top action bar, or open the jobs panel and click Download next to your finished job.

[Screenshot: download button and jobs panel with download options]

A modal lets you pick the format and what to include:

Option	Default	Effect
Format	.msd	.msd for full bundle, .csv for spreadsheet
Verdict filter	All	Restrict to Good only, or Good + Warning, etc.
Pick mode	Area Top	Intensity at peak apex vs Area Sum (matches the sidebar setting)
Include isotopologues	On (tracing only)	Add per-isotopologue columns
Include metadata	On	Sample groups, file paths, timestamps

What's in a .msd file?

A zstd-compressed Apache Arrow / Parquet bundle:

• samples.parquet — sample metadata (file path, group, injection volume, timestamps)
• compounds.parquet — per-compound metadata + verdicts
• intensities.parquet — sparse matrix of intensities (compound × sample)
• peaks.parquet — detected peak boundaries and shapes
• isotopologues.parquet — per-isotopologue intensities (if tracing was enabled)
• parameters.json — every parameter used during extraction (for reproducibility)

You don't need to know the internals — .msd files reopen in LEAF with a single drag-and-drop.

What's in a .csv file?

A wide table:

Metabolite,Formula,RetentionTime,Adduct,Verdict,WT_rep1,WT_rep2,KO_rep1,KO_rep2
Glucose,C6H12O6,5.2,M-H,good,1.23e6,1.18e6,8.4e5,9.1e5
Lactate,C3H6O3,3.1,M-H,good,4.5e5,4.7e5,9.8e5,1.05e6
...

For tracing data, isotopologue rows interleave per compound:

Metabolite,Isotopologue,WT_rep1,WT_rep2,KO_rep1,KO_rep2
Glucose,M+0,1.23e6,1.18e6,8.4e5,9.1e5
Glucose,M+1,2.4e4,2.6e4,1.8e4,2.1e4
Glucose,M+2,3.1e3,3.3e3,2.4e3,2.6e3
...

Reopening a .msd file

Drag the .msd file onto the LEAF window from anywhere — Extract page, home page, Peak Picking view, doesn't matter. LEAF detects the format and routes you to the Peak Picking view with everything restored.

Sharing results

• .msd is the canonical sharing format. It's a single self-contained file. Email it, drop it on a shared drive, or upload to your lab's storage. Anyone with LEAF can open it.
• .csv is the right choice for downstream stats software, manuscript supplementary data, or showing a colleague who doesn't have LEAF.

Untargeted exports

The Untargeted view exports .usd files (same format family as .msd) plus per-feature CSVs of intensities, retention times, and m/z values. See Untargeted analysis.

Next step

→ Isotope tracing setup — if you're running labeling experiments

Or jump to UI tour for a tour of every panel and button.