ArticleScientific reports2023
BLINK enables ultrafast tandem mass spectrometry cosine similarity scoring.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- ENVnet provides a global molecular resource of dissolved organic matter.Nature biotechnology · 2026Article
- Structure-Based Comparative Metabolomics Identifies LysoPE 15:0 as a Candidate Metabolite Marker of Influenza Virus Infection Dynamics.Molecules (Basel, Switzerland) · 2026Article
- Updated Guidance for Communicating PFAS Identification Confidence with Ion Mobility Spectrometry.Environmental science & technology · 2025Article
- Comparative analysis of continuous similarity measures for compound identification in mass spectrometry-based metabolomics.Chemometrics and intelligent laboratory systems : an international journal sponsored by the Chemometrics Society · 2025Article
- Mapping the Edges of Mass Spectral Prediction: Evaluation of Machine Learning EIMS Prediction for Xeno Amino Acids.Analytical chemistry · 2025Article
- SimMS: a GPU-accelerated cosine similarity implementation for tandem mass spectrometry.Bioinformatics (Oxford, England) · 2025Article
- The endophytic fungusCurrent research in microbial sciences · 2025Article
- Development and Application of a Multidimensional Database for the Detection of Quaternary Ammonium Compounds and Their Phase I Hepatic Metabolites in Humans.Environmental science & technology · 2024Article
- Tandem Mass Spectrometry across Platforms.Analytical chemistry · 2024Article
- Flash entropy search to query all mass spectral libraries in real time.Nature methods · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolomics has a long history of using cosine similarity to match experimental tandem mass spectra to databases for compound identification. Here we introduce the Blur-and-Link (BLINK) approach for scoring cosine similarity. By bypassing fragment alignment and simultaneously scoring all pairs of spectra using sparse matrix operations, BLINK is over 3000 times faster than MatchMS, a widely used loop-based alignment and scoring implementation. Using a similarity cutoff of 0.7, BLINK and MatchMS had practically equivalent identification agreement, and greater than 99% of their scores and matching ion counts were identical. This performance improvement can enable calculations to be performed that would typically be limited by time and available computational resources.
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Registered trials
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