Christopher M. Baxter Rath

METASPACE-ML: Context-specific metabolite annotation for imaging mass spectrometry using machine learning

Bishoy Wadie, Lachlan Stuart, Christopher M. Baxter Rath, Bernhard Drotleff et autres

Imaging mass spectrometry is a powerful technology enabling spatial metabolomics, yet metabolites can be assigned only to a fraction of the data generated. METASPACE-ML is a machine learning-based approach addressing this challenge which incorporates new scores and computationally-efficient False Discovery Rate estimation. …

de, us, dk (code pays fourni par la source)

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

Simone Zuffa, Robin Schmid, Anelize Bauermeister, Paulo Wender Portal Gomes et autres

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 search known and unknown MS/MS spectra and link them to their respective microbial producers …

us, br, Afrique du Sud, cr, ch, de, kr, gb, es, no, dk, at, mx, nl, sg (code pays fourni par la source)

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

Pieter C. Dorrestein, Simone Zuffa, Robin Schmid, Anelize Bauermeister et autres

Abstract 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 search known and unknown MS/MS spectra and link them to their respective microbial producers …

us, br, Afrique du Sud, it, cr, ch, de, kr, gb, es, no, dk, at, mx, nl, sg (code pays fourni par la source)

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

Simone Zuffa, Robin Schmid, Anelize Bauermeister, Paulo Wender Portal Gomes et autres

Abstract 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 search known and unknown MS/MS spectra and link them to their respective microbial producers …

us, br, Afrique du Sud, cr, ch, de, kr, gb, es, no, dk, at, mx, nl, sg (code pays fourni par la source)

METASPACE-ML: Context-specific metabolite annotation for imaging mass spectrometry using machine learning

Bishoy Wadie, Lachlan Stuart, Christopher M. Baxter Rath, Bernhard Drotleff et autres

Abstract Imaging mass spectrometry is a powerful technology enabling spatial metabolomics, yet metabolites can be assigned only to a fraction of the data generated. METASPACE-ML is a machine learning-based approach addressing this challenge which incorporates new scores and computationally-efficient False Discovery Rate …

de, dk (code pays fourni par la source)

Metabolic phospholipid labeling of intact bacteria enables a fluorescence assay that detects compromised outer membranes

Inga Marie Nilsson, Sheng Y. Lee, William S. Sawyer, Christopher M. Baxter Rath et autres

Gram-negative bacteria possess an asymmetric outer membrane (OM) composed primarily of lipopolysaccharides (LPSs) on the outer leaflet and phospholipids (PLs) on the inner leaflet. The loss of this asymmetry due to mutations in the LPS biosynthesis or transport pathways causes the externalization …

ch, us (code pays fourni par la source)

Two Distinct Mechanisms of Inhibition of LpxA Acyltransferase Essential for Lipopolysaccharide Biosynthesis

Wooseok Han, Xiaolei Ma, Carl J. Balibar, Christopher M. Baxter Rath et autres

The lipopolysaccharide biosynthesis pathway is considered an attractive drug target against the rising threat of multi-drug-resistant Gram-negative bacteria. Here, we report two novel small-molecule inhibitors (compounds 1 and 2 ) of the acyltransferase LpxA, the first enzyme in the lipopolysaccharide biosynthesis pathway. …

us (code pays fourni par la source)

Two distinct mechanisms of small molecule inhibition of LpxA acyltransferase essential for lipopolysaccharide biosynthesis

Wooseok Han, Xiaolei Ma, Carl J. Balibar, Christopher M. Baxter Rath et autres

The paper with the doi 10.1101/850305 has been removed as a result of a technical error. The paper is available on bioRxiv under this doi: 10.1101/2019.12.14.850305.

ch (code pays fourni par la source)

Two distinct mechanisms of small molecule inhibition of LpxA acyltransferase essential for lipopolysaccharide biosynthesis

Wooseok Han, Xiaolei Ma, Carl J. Balibar, Christopher M. Baxter Rath et autres

The lipopolysaccharide biosynthesis pathway is considered an attractive drug target against the rising threat of multidrug-resistant Gram-negative bacteria. Here, we report two novel small-molecule inhibitors (compounds 1 and 2) of the acyltransferase LpxA, the first enzyme in the lipopolysaccharide biosynthesis pathway. We …

ch (code pays fourni par la source)

A Unified Framework for the Incorporation of Bioorthogonal Compound Exposure Probes within Biological Compartments

Benjamin Spangler, Shengtian Yang, Christopher M. Baxter Rath, Folkert Reck et autres

Compartmentalization is a crucial facet of many biological systems, and key aspects of cellular processes rely on spatial segregation within the cell. While many drug targets reside in specific intracellular compartments, the tools available for assessing compound exposure are generally limited to …

us (code pays fourni par la source)

Targeted lipopolysaccharide biosynthetic intermediate analysis with normal-phase liquid chromatography mass spectrometry

William S. Sawyer, Lisha Wang, Tsuyoshi Uehara, Pramila Tamrakar et autres

Lipopolysacharride (LPS) forms the outer leaflet of the outer membrane in Gram-negative bacteria and contributes to the permeability barrier and immune response. In this study, we established a method for monitoring the LPS biosynthetic intermediates of the Raetz pathway (lpxA-lpxK) in Escherichia …

us (code pays fourni par la source)

Metabolic labeling of phospholipids in intact bacteria enables a fluorescence assay to detect loss of outer membrane asymmetry

Inga Marie Nilsson, Sheng Y. Lee, William S. Sawyer, Christopher M. Baxter Rath et autres

Gram-negative bacteria possess an asymmetric outer membrane (OM) composed primarily of lipopolysaccharides (LPS) on the outer leaflet and phospholipids (PLs) on the inner leaflet. Loss of asymmetry due to mutation in the lipopolysaccharide (LPS) biosynthesis or transport pathways causes PLs to be …