Frequently Asked Questions
What does LEAF do?
LEAF processes targeted LC-MS metabolomics data. It extracts ion chromatograms from a compound list, performs peak picking, assigns quality verdicts, supports isotope-tracing review, and produces interactive visualizations. Targeted analyses accept Thermo .raw, .mzml, and .mzml.gz files in the current user-facing workflow. Results export as .msd archives or flat .csv tables.
Who is LEAF for?
Researchers running LC-MS metabolomics, including:
- Users who prefer a graphical interface over a scripting environment
- Routine targeted panels in a lab setting
- ¹³C, ¹⁵N, ²H, ¹⁸O, or ³⁴S tracing experiments
No Python, R, or command-line experience is required to operate LEAF.
How does LEAF relate to Xcalibur, Skyline, MZmine, and El-MAVEN?
LEAF is intended to complement, not replace, established tools. Xcalibur remains the reference for raw-data inspection on Thermo instruments; Skyline provides extensive manual curation features for targeted proteomics and metabolomics; MZmine and El-MAVEN cover overlapping workflows. LEAF's documented scope in this manual is batch targeted quantification, isotope tracing, quality review, and integrated visualization within a single browser-based interface.
Where are input and processed data stored?
Desktop install: LEAF binds to 127.0.0.1 (loopback only) and makes no outbound network requests. RAW files and processed data remain on the local filesystem.
Hosted (MINT): under development. When enabled, data will reside on the lab server and access will be governed by MINT controls. For current use, local installs keep RAW files and processed data on the local filesystem.
Can I use LEAF on a non-Thermo instrument?
Yes, if the instrument data are exported as mzML. LEAF targeted runs accept .mzml and .mzml.gz in addition to Thermo .raw. The SEED reader has broader vendor-reader work, but this manual documents the current user-facing targeted workflow.
How big a dataset can LEAF handle?
It depends on file size, storage speed, reader backend, compound count, and whether MS² extraction is enabled. Targeted runs scale mainly with the number of compounds and samples.
For a rough check, start with a small folder and watch the floating progress button. If a modest targeted run takes much longer than expected, see Troubleshooting.
For very large datasets (1000+ samples), use the Rust backend (Settings → Advanced) and run on a machine with 32 GB+ RAM.
What is an .msd file?
An .msd file is LEAF's native targeted result archive. It stores the processed dataset, selected peaks, quality information, isotope-tracing data when present, and run parameters in one self-contained file. Dragging the archive into LEAF reopens the Peak Picking view with the analysis restored.
How are analyses shared with collaborators?
The .msd archive is the sharing format. A collaborator with a LEAF installation using the same major version can open the archive and view the stored charts, parameters, peaks, and quality scores without re-extraction.
Does LEAF do natural-abundance correction for tracing?
Yes, for the current targeted tracing surface. In Peak Picking, configure tracer purity from the isotopologue-bar gear popover or the export panel, then enable natural-abundance correction for the bar plot or corrected CSV export. The command line supports the same path with leaf targeted --correct --tracer 13C:0.99.
Current correction support is intentionally narrow: high-resolution correction for tracer elements C, H, and N. Position-specific tracers, low-resolution correction, and multi-heavy-isotope elements such as O and S are not part of the current correction surface.
How do I update LEAF?
leaf update --dry-run
leaf updateleaf update resolves the latest compatible wheel from GitHub Releases for the current operating system and Python version. Use --dry-run to preview the resolved wheel before installing. For a specific release or local wheel:
leaf update --github-release v0.5.7
leaf update --package ./leaf-0.5.7-*.whlCan I access the source code?
Yes. The source code is available in the MorscherLab/LEAF repository, and this manual is maintained in MorscherLab/LEAF-docs.
How do I cite LEAF in a paper?
A citable preprint / DOI is forthcoming. Until then, cite the LEAF version used in the analysis and acknowledge the Morscher Lab.
Where can I report bugs or request features?
Contact the Morscher Lab or the local LEAF administrator. Include the LEAF version, operating system, and steps required to reproduce the issue.