The Science Behind VeroMass
Rigorous, published methodology you can trust.
Three orthogonal gates. One definitive answer.
VeroMass does not return ranked candidates. Every identification passes through three independent verification gates, each comparing the submitted feature against a physically measured standard. Only when all three gates agree do we report MSI Level 1a.
Mass Accuracy Gate
Retention Time Gate
MS² Fragmentation Gate
40,112 standards, physically measured.
Every standard in the VeroMass library was sourced as a high-purity reference compound, dissolved, injected, and analysed on a calibrated LC-MS/MS system. No spectra are predicted or computationally generated.
The library spans the major classes of plant and microbial secondary metabolism:
Flavonoids
Flavonols, flavones, flavanones, isoflavones, anthocyanins, biflavonoids — aglycones and O- and C-glycosides across all substitution patterns.
Phenolic Acids & Hydroxycinnamates
Caffeic, ferulic, sinapic, coumaric acids and their quinate, shikimate, and sugar esters, including chlorogenic acid isomers.
Alkaloids
Tropane, isoquinoline, indole, and pyrrolizidine alkaloids, each with characterised fragment pathways.
Terpenoids & Saponins
Mono-, sesqui-, di-, and triterpenoids, including saponins with complex sugar chains.
Lipids & Fatty Acids
Oxylipins, free fatty acids, glycerolipids, and phospholipids relevant to plant membrane biology.
Amino Acids & Derivatives
Proteinogenic and modified amino acids, betaines, and small-molecule nitrogen metabolites.
Why Level 1a matters.
The Metabolomics Standards Initiative defines four confidence levels for metabolite identification. Level 1a requires an exact match on mass, fragmentation, and retention time against a standard that physically exists. VeroMass delivers Level 1a, not a ranked list.
Three orthogonal gates (mass, RT, MS²) agree against an authentic standard. Verified in both ESI+ and ESI−.
Matched to a library spectrum or diagnostic evidence, but no authentic standard is available for co-elution verification.
Assigned to a compound class based on spectral similarity or predicted properties. A hypothesis, not an identification.
What Level 1a is not
In-silico tools that return ranked candidates based on predicted fragmentation do not reach Level 1a. However sophisticated the scoring, without a measured standard for RT and MS² validation, the answer is a probability, not an identity. VeroMass offers measured evidence, not ranked guesses.
Measured performance, not promises.
Every gate has defined thresholds that are applied uniformly across the entire library. The numbers below represent the validation set from the full production library.
Cosine Threshold
≥ 0.85 minimum cosine score between submitted and library MS² spectrum. The library-wide median cosine for true matches is 0.965, well above the threshold.
Mass Accuracy
Precursor mass tolerance of ≤ 9 mDa. The median observed error across all standards in both polarities is ±0.6 mDa, corresponding to sub-ppm accuracy on most small molecules.
Retention Time Tolerance
RT gate set at ≤ 0.3 min vs. the authentic standard. Co-elution is verified by the RT predictor (R² = 0.986) and cross-checked against the measured library RT.
Dual-Polarity Coverage
Every standard measured in both ESI+ and ESI−. Many metabolites ionise preferentially in one polarity; dual coverage ensures no compound is missed due to ionisation bias.
Collision Energy Variation
Each standard is fragmented at multiple collision energies (20, 35, 50 eV) to capture energy-dependent spectral variation and ensure robust matching across instrument types.
Batch Reproducibility
QC standards are reinjected every 20 samples to monitor mass drift, RT shift, and signal intensity. Acceptance criteria: mass error ≤ 3 mDa, RT shift ≤ 0.1 min over the entire batch.
Peer-reviewed and independently validated.
The methodology behind VeroMass and the library construction pipeline has been published in leading analytical chemistry and metabolomics journals.
Large-scale LC-MS/MS library construction for plant metabolomics: 40,000+ authenticated standards
Three-gate verification for MSI Level 1a metabolite identification in untargeted metabolomics
Comprehensive annotation of the wheat root metabolome using multi-gate spectral library matching
Current state of spectral library matching in untargeted metabolomics
VeroMass: scalable cloud-based metabolomics annotation with real-time spectral networking
Target fishing in complex plant extracts guided by MSI Level 1a spectral networks
Experience the science firsthand.
Upload your own LC-MS/MS run and see Level 1a identifications generated in real time, backed by measured standards and three orthogonal verification gates.