Export Targeted Results

Export the processed targeted dataset as a LEAF archive for review or as a flat table for downstream statistical analysis.

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 the completed job.

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

A modal provides controls for format selection and included fields:

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

.msd archive

The .msd file is LEAF's native targeted result archive. It stores:

• Sample metadata and file provenance
• Compound metadata and quality verdicts
• Extracted intensities and selected peaks
• Isotopologue intensities when tracing is enabled
• Extraction and scoring parameters required for reproducibility

The archive reopens in LEAF with drag-and-drop.

CSV table

The standard CSV is 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
# additional metabolites omitted

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
# additional isotopologues omitted

Reopening a .msd file

Drag the .msd file onto the LEAF window. LEAF detects the format and opens the Peak Picking view with the stored targeted analysis restored.

Sharing results

• .msd is the canonical sharing format. It is a single self-contained file that can be opened by another LEAF installation.
• .csv is suitable for downstream statistical software, manuscript supplementary data, or collaborators who do not use LEAF.

Lab-wide storage

LEAF can persist .msd archives directly to an S3-compatible bucket (AWS S3, MinIO, Ceph RGW) so results are reachable from any configured LEAF instance without manual copying. Configure storage under Settings → Storage or with environment variables. See Storage backend.

Also from a script

Saving and reopening a .msd from Python:

from leaf.analyzer import Samples
samples = Samples.load("analysis.msd")
# inspect / mutate ...
samples.save("analysis-revised.msd")

→ Python recipes

Next step

→ Isotope tracing setup — for stable-isotope labeling experiments

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