Glossary

A short reference for the LC-MS terms you'll see in LEAF, written for someone who isn't a mass spectrometrist.

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 picked up a sodium. The adduct determines the m/z LEAF looks for.

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 threshold. LEAF flags compounds with detection rate < 20% as "Poor".

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.

F

Feature (untargeted) A peak detected without prior knowledge — characterized by its m/z and retention time, but no name yet. The Untargeted view is a list of features.

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 where you feed cells/tissues a labeled substrate (e.g., ¹³C-glucose) and measure how the label propagates through 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". Configurable in the Extract page (default 100,000).

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 runs as a plugin under MINT in the hosted lab version. (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 where peaks start and end in a chromatogram, and characterizing their shape. LEAF offers methods v1 (basic), v2 (smoothed), v4 (advanced — recommended).

Polarity Mass-spectrometer mode — POS (positive) detects positively-charged ions; NEG (negative) detects negatively-charged. Must match your 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 (use it), Warning (review it), Poor (probably exclude).

R

RAW file Thermo Fisher's native LC-MS file format (.raw). The input to every LEAF workflow.

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

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

SNR (Signal-to-Noise Ratio) How strong a peak is relative to the baseline noise. Higher = more confident the peak is real. Configurable threshold on the Extract page.

T

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

U

Untargeted analysis Discovering features without a prior list. Slower, gives you a triage table to find candidates.

.usd file LEAF's native bundle for untargeted results. Same format family as .msd but contains feature data instead of compound data.