Glossary

A short reference for LC-MS terms used in the targeted LEAF workflow.

A

Adduct The ion form a molecule takes during ionization. M-H means the molecule lost a proton (negative mode); M+H means it gained one (positive mode); M+Na means it formed a sodium adduct. The adduct determines the m/z extracted by LEAF.

Alignment Adjusting retention times across samples so the same compound peaks at the same RT in every sample. LEAF aligns automatically during peak picking.

Apex The highest point of a chromatographic peak. "Area Top" pick mode uses the apex intensity.

C

Chromatogram A plot of signal intensity vs time. The "EIC" (extracted ion chromatogram) shows the signal for one specific m/z over the LC run.

D

Detection rate Percentage of samples in which a compound was detected above the configured threshold.

E

EIC (Extracted Ion Chromatogram) The chromatogram for a single m/z (or a narrow m/z window). LEAF builds an EIC for every compound × sample combination.

Formula Molecular formula of a compound, like C6H12O6 for glucose. LEAF uses it to compute the exact mass.

I

Integration Calculating the area under a peak. Two modes:

• Area Top — peak height at the apex
• Area Sum — total integrated area across the peak boundary

Isotopologue Same molecule, different number of heavy isotopes. M+0 is the unlabeled form; M+1 has one extra mass unit (one ¹³C, ¹⁵N, etc.); M+2 has two; and so on.

Isotope tracing An experiment in which a labeled substrate (e.g., ¹³C-glucose) is supplied to cells or tissues and label incorporation is measured across metabolism. LEAF measures isotopologue distributions per metabolite.

L

LC-MS (Liquid Chromatography–Mass Spectrometry) The two-step technique LEAF processes data from. LC separates compounds in time; MS measures their mass.

LOD (Limit of Detection) Minimum signal level required for a peak to count as detected in quality scoring. In the Extract page, Auto derives the LOD from the intensity threshold.

leaf serve (deprecated) Older docs and forum posts referenced leaf serve as the launch command. The actual entry point is leaf webui run (foreground) or leaf webui start (daemon). See leaf webui.

M

Mass tolerance How far an observed m/z can deviate from the expected m/z and still be considered the same compound. Expressed in ppm (parts per million). Lower = stricter. 5 ppm is a typical default.

Metabolomics Measuring small-molecule metabolites in biological samples. LEAF is built specifically for this use case.

MINT The Morscher Lab's internal data platform. LEAF's MINT plugin deployment path is under development and is not yet available for general use. (Acronym originally stood for the lab database; rebranded 2026.)

MS1 First-stage mass spectrometry — measures the parent ion's m/z. LEAF works primarily with MS1 data.

MS2 Second-stage MS — fragments the parent ion and measures the fragments. Used for compound identification. LEAF supports MS2 spectral matching against mzVault libraries.

m/z (mass-to-charge ratio) What a mass spectrometer actually measures. For singly-charged ions (the common case in metabolomics), m/z ≈ mass.

.msd file LEAF's native bundle for targeted analysis results. Contains intensities, peaks, quality scores, parameters. zstd-compressed Arrow/Parquet.

mzVault A SQLite-based spectral library format from Thermo. Used for MS2 identification.

P

Peak picking Detecting peak positions and boundaries in a chromatogram.

Polarity Mass-spectrometer mode — POS (positive) detects positively charged ions; NEG (negative) detects negatively charged ions. The setting must match the acquisition method.

ppm (parts per million) Unit for mass tolerance. 5 ppm at m/z 200 = 0.001 Da. Lower ppm = stricter matching.

Q

Quality verdict LEAF's per-compound assessment. Good indicates a reliable signal, Warning indicates a result requiring review, and Poor indicates low confidence.

R

RAW file Thermo Fisher's native LC-MS file format (.raw). Targeted LEAF runs also accept .mzml and .mzml.gz.

RetentionTime / RT When a compound elutes from the LC column, in minutes. LEAF uses the expected RT to know where to look for each metabolite.

RT alignment Compensating for small RT shifts between samples (column aging, temperature drift, etc.). Done automatically during extraction.

S

SEED (Spectral Extraction & Encoding Driver) The Rust library LEAF uses to read .raw and mzML-family files, especially on macOS and Linux where it is the default reader backend. It replaces the legacy oxion codename. See SEED.

SEM (Standard Error of the Mean) Error bars in the isotopologue chart show mean ± SEM per sample group.

SNR (Signal-to-Noise Ratio) Peak strength relative to baseline noise. Higher values indicate greater confidence that the peak is distinguishable from noise. Configurable threshold on the Extract page.

T

Targeted analysis Quantifying a known list of compounds. Requires a metabolite CSV. Fast and reproducible.