Linguistics

Philosophy

Biology

Materials science

Chromatography

Operating system

Computer science

Computational biology

Tandem

Pattern recognition (psychology)

Artificial intelligence

Composite material

Simile

Mass spectrometry

Chemistry

Metaphor

Tandem mass spectrometry

Fragmentation (computing)

Nature Communications

Interrelating small molecules according to their aligned fragmentation spectra is central to tandem mass spectrometry-based untargeted metabolomics. Current alignment algorithms do not provide statistical significance and compounds that have multiple delocalized structural differences and therefore often fail to have their fragment ions aligned. Here we align fragmentation spectra with both statistical significance and allowance for multiple chemical differences using Significant Interrelation of MS/MS Ions via Laplacian Embedding (SIMILE). SIMILE yields spectral alignment inferred structural connections in molecular networks that are not found with cosine-based scoring algorithms. In addition, it is now possible to rank spectral alignments based on p-values in the exploration of structural relationships between compounds and enhance the chemical connectivity that can be obtained with molecular networking.

SIMILE enables alignment of tandem mass spectra with statistical significance