Yasin El Abiead
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View article: The undiscovered natural product potential of Actinomycetes
The undiscovered natural product potential of Actinomycetes Open
Actinomycetes have been a cornerstone species for the discovery of bioactive natural products with applications in pharmacotherapy and biotechnology. To expand the experimental evidence of their biosynthetic potential, we collected liquid-…
View article: A Perspective on Unintentional Fragments and Their Impact on the Dark Metabolome, Untargeted Profiling, Molecular Networking, Public Data, and Repository Scale Analysis
A Perspective on Unintentional Fragments and Their Impact on the Dark Metabolome, Untargeted Profiling, Molecular Networking, Public Data, and Repository Scale Analysis Open
View article: Bridging Complexity and Accessibility in Metabolomics with MetaboApps
Bridging Complexity and Accessibility in Metabolomics with MetaboApps Open
Untargeted metabolomics is a powerful approach for exploring the chemical diversity and dynamics of biological systems. However, the types of questions that can be addressed depend not only on experimental design but also on the data proce…
View article: mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format
mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format Open
Advances in mass spectrometry (MS) instrumentation, including higher resolution, faster scan speeds, and improved sensitivity, have dramatically increased the data volume and complexity. The adoption of imaging and ion mobility further amp…
View article: PREPRINT "Comparability of Liquid Chromatography Tandem Mass Spectrometry Analysis of Dissolved Organic Matter Across Laboratories"
PREPRINT "Comparability of Liquid Chromatography Tandem Mass Spectrometry Analysis of Dissolved Organic Matter Across Laboratories" Open
Non-targeted liquid-chromatography tandem high-resolution mass-spectrometry (LC-MS/MS) is increasingly applied for the structure-resolved chemical analysis of dissolved organic matter (DOM). With new developments in mass spectrometry instr…
View article: A Perspective on Unintentional Fragments and their Impact on the Dark Metabolome, Untargeted Profiling, Molecular Networking, Public Data, and Repository Scale Analysis.
A Perspective on Unintentional Fragments and their Impact on the Dark Metabolome, Untargeted Profiling, Molecular Networking, Public Data, and Repository Scale Analysis. Open
In/post-source fragments (ISFs) arise during electrospray ionization or ion transfer in mass spectrometry when molecular bonds break, generating ions that can complicate data interpretation. Although ISFs have been recognized for decades, …
View article: An evaluation methodology for machine learning-based tandem mass spectra similarity prediction
An evaluation methodology for machine learning-based tandem mass spectra similarity prediction Open
Background Untargeted tandem mass spectrometry serves as a scalable solution for the organization of small molecules. One of the most prevalent techniques for analyzing the acquired tandem mass spectrometry data (MS/MS) - called molecular …
View article: Influence of perinatal ampicillin exposure on maternal fecal microbial and metabolic profiles
Influence of perinatal ampicillin exposure on maternal fecal microbial and metabolic profiles Open
Indirect exposure to antibiotics during early life, via maternal intrapartum antibiotic prophylaxis (IAP) or postpartum maternal antibiotic usage, is increasingly common and has been epidemiologically linked to altered growth and immune de…
View article: Metabolome trajectories in male and female athletes
Metabolome trajectories in male and female athletes Open
View article: The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids
The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids Open
N-Acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N-acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference spe…
View article: Enabling pan-repository reanalysis for big data science of public metabolomics data
Enabling pan-repository reanalysis for big data science of public metabolomics data Open
View article: MS/MS Mass Spectrometry Filtering Tree for Bile Acid Isomer Annotation
MS/MS Mass Spectrometry Filtering Tree for Bile Acid Isomer Annotation Open
Bile acids are essential steroids regulating immunity, nutrient absorption, insulin, appetite, and body temperature. Their structural diversity is vast, but due to spectral similarities, MS/MS spectral matching often fails to resolve isome…
View article: MS-RT: A Method for Evaluating MS/MS Clustering Performance for Metabolomics Data
MS-RT: A Method for Evaluating MS/MS Clustering Performance for Metabolomics Data Open
The clustering of tandem mass spectra (MS/MS) is a crucial computational step to deduplicate repeated acquisitions in data-dependent experiments. This technique is essential in untargeted metabolomics, particularly with high-throughput mas…
View article: Discovery of metabolites prevails amid in-source fragmentation
Discovery of metabolites prevails amid in-source fragmentation Open
View article: The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns
The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns Open
Space habitation provides unique challenges in built environments isolated from Earth. We produced a 3D map of the microbes and metabolites throughout the United States Orbital Segment (USOS) of the International Space Station (ISS) with 8…
View article: The microbiome diversifies<i>N</i>-acyl lipid pools - including short-chain fatty acid-derived compounds
The microbiome diversifies<i>N</i>-acyl lipid pools - including short-chain fatty acid-derived compounds Open
N -acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N -acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference s…
View article: Structural annotation of full-scan MS data: A unified solution for LC-MS and MS imaging analyses
Structural annotation of full-scan MS data: A unified solution for LC-MS and MS imaging analyses Open
Public liquid chromatography-mass spectrometry (LC-MS) and MS imaging metabolomics data repositories contain millions of files, with over 40% of them consisting solely of MS1 (full-scan) information, creating a significant gap in data reus…
View article: Empirically establishing drug exposure records directly from untargeted metabolomics data
Empirically establishing drug exposure records directly from untargeted metabolomics data Open
Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based GNPS Drug Library. This resource integ…
View article: Receptor and metabolic insights on the ability of caffeine to prevent alcohol-induced stimulation of mesolimbic dopamine transmission
Receptor and metabolic insights on the ability of caffeine to prevent alcohol-induced stimulation of mesolimbic dopamine transmission Open
View article: Leptochelins A–C, Cytotoxic Metallophores Produced by Geographically Dispersed <i>Leptothoe</i> Strains of Marine Cyanobacteria
Leptochelins A–C, Cytotoxic Metallophores Produced by Geographically Dispersed <i>Leptothoe</i> Strains of Marine Cyanobacteria Open
Metals are important cofactors in the metabolic processes of cyanobacteria, including photosynthesis, cellular respiration, DNA replication, and the biosynthesis of primary and secondary metabolites. In adaptation to the marine environment…
View article: Receptor and metabolic insights on the ability of caffeine to prevent alcohol-induced stimulation of mesolimbic dopamine transmission
Receptor and metabolic insights on the ability of caffeine to prevent alcohol-induced stimulation of mesolimbic dopamine transmission Open
The consumption of alcohol and caffeine affects the lives of billions of individuals worldwide. Although recent evidence indicates that caffeine impairs the reinforcing properties of alcohol, a characterization of its effects on alcohol-st…
View article: ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization
ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization Open
Untargeted tandem mass spectrometry (MS/MS) has become a high-throughput method to measure small molecules in complex samples. One key goal is the transformation of these MS/MS spectra into chemical structures. Computational techniques suc…
View article: Enabling pan-repository reanalysis for big data science of public metabolomics data
Enabling pan-repository reanalysis for big data science of public metabolomics data Open
Public untargeted metabolomics data is a growing resource for metabolite and phenotype discovery; however, accessing and utilizing these data across repositories pose significant challenges. Therefore, we've developed pan-repository univer…
View article: Leptochelins A-C, Cytotoxic Metallophores Produced by Geographically Dispersed Leptothoe Strains of Marine Cyanobacteria
Leptochelins A-C, Cytotoxic Metallophores Produced by Geographically Dispersed Leptothoe Strains of Marine Cyanobacteria Open
Metals are important co-factors in the metabolic processes of cyanobacteria including photosynthesis, cellular respiration, DNA replication, and the biosynthesis of primary and secondary metabolites. In adaptation to the marine environment…
View article: The underappreciated diversity of bile acid modifications
The underappreciated diversity of bile acid modifications Open
The repertoire of modifications to bile acids and related steroidal lipids by host and microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource of tandem mass spectrometry (MS/M…
View article: ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization
ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization Open
Untargeted tandem mass spectrometry (MS/MS) has become a high-throughput method to measure small molecules in complex samples. One key goal is the transformation of these MS/MS spectra into chemical structures. Computational techniques suc…
View article: microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data
microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data Open
View article: The Hitchhiker’s Guide to Statistical Analysis of Feature-based Molecular Networks from Non-Targeted Metabolomics Data
The Hitchhiker’s Guide to Statistical Analysis of Feature-based Molecular Networks from Non-Targeted Metabolomics Data Open
Feature-Based Molecular Networking (FBMN) is a popular analysis approach for LC-MS/MS-based non-targeted metabolomics data. While processing LC-MS/MS data through FBMN is fairly streamlined, downstream data handling and statistical interro…
View article: A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data
A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data Open
MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can s…
View article: A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data
A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data Open
MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can s…