Annotating metabolite mass spectra with domain-inspired chemical formula transformers
Metabolomics studies have identified small molecules that mediate cell signaling,
competition and disease pathology, in part due to large-scale community efforts to measure …
competition and disease pathology, in part due to large-scale community efforts to measure …
Prefix-tree decoding for predicting mass spectra from molecules
Computational predictions of mass spectra from molecules have enabled the discovery of
clinically relevant metabolites. However, such predictive tools are still limited as they occupy …
clinically relevant metabolites. However, such predictive tools are still limited as they occupy …
MIST-CF: Chemical formula inference from tandem mass spectra
Chemical formula annotation for tandem mass spectrometry (MS/MS) data is the first step
toward structurally elucidating unknown metabolites. While great strides have been made …
toward structurally elucidating unknown metabolites. While great strides have been made …
Spectrum of the past
MA Skinnider - Nature Reviews Chemistry, 2024 - nature.com
Thirty-four years ago, Curry and Rumelhart described a neural network-based approach to
annotate tandem mass spectra. Their ideas foreshadowed several important developments …
annotate tandem mass spectra. Their ideas foreshadowed several important developments …
Contrastive learning-based embedder for the representation of tandem mass spectra
Tandem mass spectrometry (MS/MS) shows great promise in the research of metabolomics,
providing an abundance of information on compounds. Due to the rapid development of …
providing an abundance of information on compounds. Due to the rapid development of …
De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments
K Eloff, K Kalogeropoulos, O Morell, A Mabona… - bioRxiv, 2023 - biorxiv.org
Bottom-up mass spectrometry-based proteomics is challenged by the task of identifying the
peptide that generates a tandem mass spectrum. Traditional methods that rely on known …
peptide that generates a tandem mass spectrum. Traditional methods that rely on known …
MS2Mol: A transformer model for illuminating dark chemical space from mass spectra
The ability to identify small molecules in complex samples from their mass spectra is among
the grand challenges of analytical chemistry. Improvements to this ability could significantly …
the grand challenges of analytical chemistry. Improvements to this ability could significantly …
Mass2SMILES: deep learning based fast prediction of structures and functional groups directly from high-resolution MS/MS spectra.
Modern mass spectrometry-based metabolomics generates vast amounts of mass spectral
data as part of the chemical inventory of biospecimens. Annotation of the resulting MS/MS …
data as part of the chemical inventory of biospecimens. Annotation of the resulting MS/MS …
Machine Learning Methods for Discovering Metabolite Structures from Mass Spectra
SL Goldman - 2024 - dspace.mit.edu
Small molecule metabolites mediate myriad biological and environmental phenomena
across host-microbiome interactions, plant chemistry, cancer biology, and various other …
across host-microbiome interactions, plant chemistry, cancer biology, and various other …
De novo peptide sequencing with InstaNovo: Diffusion-powered, peptide identification for large scale proteomics experiments
T Jenkins, K Eloff, K Kalogeropoulos, O Morell… - 2024 - researchsquare.com
Bottom-up mass spectrometry-based proteomics is challenged by the task of identifying the
peptide that generates a tandem mass spectrum. Traditional methods that rely on known …
peptide that generates a tandem mass spectrum. Traditional methods that rely on known …