Software

Software 

Researchers at Pacific Northwest National Laboratory are advancing reference-free metabolomics—the identification of metabolites and related small molecules without reliance on data from analysis of pure reference standards—using predicted molecular properties and matching to experimental data from multi-dimensional analysis. PNNL’s unique approach relies on multiple experimental data types, including accurate mass, isotopic distribution, collision cross section, fragmentation spectra, and ion infrared spectra. Experimental values are then compared to entries inreference libraries constructed through computational predictions. 

The approach includes four key tools: 

• Data Extraction for Integrated Multidimensional Spectrometry (DEIMoS), a modular software tool that can extract features from data collected on multi-dimensional analytical platforms. 
• HP-Ω, a molecular dynamics tool for precisely calculating CCS based on differences in rotational energy transfer during ion-molecule collisions.   
• QC-GN²oMS², a graph neural network for MS/MS spectra prediction using quantum chemistry. 
• DarkChem, a variational autoencoder that learns a continuous numerical or latent representation of molecular structure, which can characterize and expand reference libraries. 

Learn more about the patented tools available for licensing. 

Databases

Collision cross-section library for metabolites and other small molecules.