ArticleNature communications2022
SIMILE enables alignment of tandem mass spectra with statistical significance.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Zero-shot de novo peptide sequencing with open posttranslational modification discovery.Nature biotechnology · 2026Article
- Cross ionization mode chemical similarity prediction between tandem mass spectra in metabolomics.Nature communications · 2026Article
- Review
- A large language model for deriving spectral embeddings for accurate compound identification in mass spectrometry.Communications chemistry · 2025Article
- mineMS2: annotation of spectral libraries with exact fragmentation patterns.Journal of cheminformatics · 2025Article
- ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization.Journal of the American Society for Mass Spectrometry · 2024Article
- Deep learning prediction of electrospray ionization tandem mass spectra of chemically derived molecules.Nature communications · 2024Article
- Network Topology Evaluation and Transitive Alignments for Molecular Networking.Journal of the American Society for Mass Spectrometry · 2024Article
- The changing metabolic landscape of bile acids - keys to metabolism and immune regulation.Nature reviews. Gastroenterology & hepatology · 2024Review
- TransExION: a transformer based explainable similarity metric for comparing IONS in tandem mass spectrometry.Journal of cheminformatics · 2024Article
- The hidden treasures in endophytic fungi: a comprehensive review on the diversity of fungal bioactive metabolites, usual analytical methodologies, and applications.Archives of microbiology · 2024Review
- Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics.Nature communications · 2023Article
- BLINK enables ultrafast tandem mass spectrometry cosine similarity scoring.Scientific reports · 2023Article
- BUDDY: molecular formula discovery via bottom-up MS/MS interrogation.Nature methods · 2023Article
- Review
- Artificial intelligence in microbial natural product drug discovery: current and emerging role.Natural product reports · 2022Review
- Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools.Metabolomics : Official journal of the Metabolomic Society · 2022Review
- The critical role that spectral libraries play in capturing the metabolomics community knowledge.Metabolomics : Official journal of the Metabolomic Society · 2022Review
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Authors and funding
8 authors.
Funding
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Abstract
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.
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