Related papers: iMet: A computational tool for structural annotati…
The identification of metabolites from complex biological samples often involves matching experimental mass spectrometry data to signatures of compounds derived from massive chemical databases. However, misidentifications may result due to…
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 solving this problem, the current state-of-the-art method…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
Metabolites, small molecules that are involved in cellular reactions, provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually relies on tandem mass spectrometry to identify the thousands of…
Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism. Today, the vast majority of metabolites remain unknown, in particular for non-model organisms. Mass spectrometry is one of the predominant…
High throughput metabolomics data are fraught with both non-ignorable missing observations and unobserved factors that influence a metabolite's measured concentration, and it is well known that ignoring either of these complications can…
Compound identification and structure annotation from mass spectra is a well-established task widely applied in drug detection, criminal forensics, small molecule biomarker discovery and chemical engineering. We propose SpecTUS: Spectral…
Untargeted metabolomics based on liquid chromatography-mass spectrometry technology is quickly gaining widespread application given its ability to depict the global metabolic pattern in biological samples. However, the data is noisy and…
Electrospray tandem mass spectrometry (ESI-MS/MS) is commonly used in high throughput metabolomics. One of the key obstacles to the effective use of this technology is the difficulty in interpreting measured spectra to accurately and…
Many diseases cause significant changes to the concentrations of small molecules (aka metabolites) that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile". This…
A key challenge in metabolomics is annotating measured spectra from a biological sample with chemical identities. Currently, only a small fraction of measurements can be assigned identities. Two complementary computational approaches have…
The diverse metabolic pathways are fundamental to all living organisms, as they harvest energy, synthesize biomass components, produce molecules to interact with the microenvironment, and neutralize toxins. While discovery of new…
Motivation: A major challenge in metabolomics is annotation: assigning molecular structures to mass spectral fragmentation patterns. Despite recent advances in molecule-to-spectra and in spectra-to-molecular fingerprint prediction (FP),…
Identifying the interaction targets of bioactive compounds is a foundational element for deciphering their pharmacological effects. Target prediction algorithms equip researchers with an effective tool to rapidly scope and explore potential…
Motivation: NMR spectra are widely used in metabolomics to obtain metabolite profiles in complex biological mixtures. Common methods used to assign and estimate concentrations of metabolites involve either an expert manual peak fitting or…
Background. Emerging technologies now allow for mass spectrometry based profiling of up to thousands of small molecule metabolites (metabolomics) in an increasing number of biosamples. While offering great promise for revealing insight into…
Liquid chromatography mass spectrometry (LC-MS)-based metabolomics and exposomics aim to measure detectable small molecules in biological samples. The results facilitate hypothesis-generating discovery of metabolic changes and disease…
Cancer is a heterogeneous disease with different combinations of genetic and epigenetic alterations driving the development of cancer in different individuals. While these alterations are believed to converge on genes in key cellular…
Untargeted metabolomics generates large volumes of tandem mass spectrometry (MS/MS) data and computational annotations that can reveal molecular mechanisms across organisms and environments. Public reuse has improved through harmonized…
The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of…