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Showing 1–10 of 10 results
Advanced filters: Author: Daniel Pluskal Clear advanced filters

  • The Mass Spectrometry Query Language (MassQL) is an open-source language that enables instrument-independent searching across mass spectrometry data for complex patterns of interest via concise and expressive queries without the need for programming skills.

    • Tito Damiani
    • Alan K. Jarmusch
    • Mingxun Wang
    Research
    Nature Methods
    Volume: 22, P: 1247-1254

  • The authors present a workflow integrating metabolic perturbations with protein structural analysis to identify drug off-targets, demonstrating how combining machine learning methods with mechanistic analyses can benefit off-target identification.

    • Sourav Chowdhury
    • Daniel C. Zielinski
    • Eugene I. Shakhnovich
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-14

  • NanoLuc luciferase is a popular bioluminescent enzyme, but the molecular details of its mechanism of action on luciferins such as coelenterazine remained elusive. Here the authors use, protein crystal structures and biochemical analyses to provide an atomistic description of its catalytic mechanism and allosteric behaviour.

    • Michal Nemergut
    • Daniel Pluskal
    • Martin Marek
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-20

  • Molecular networking connects molecules based on their fragment ion mass spectra (MS2), but may leave adduct species from the same molecular family separate. To address this issue, the authors develop a networking approach that fuses MS1- and MS2-based networks and integrate it into the GNPS environment.

    • Robin Schmid
    • Daniel Petras
    • Pieter C. Dorrestein
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-12

  • Directed evolution commonly relies on point mutations but InDels frequently occur in evolution. Here the authors report a protein-engineering framework based on InDel mutagenesis and fragment transplantation resulting in greater catalysis and longer glow-type bioluminescence of the ancestral luciferase.

    • Andrea Schenkmayerova
    • Gaspar P. Pinto
    • Jiri Damborsky
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-16

  • Renilla luciferase is a popular bioluminescent enzyme, but the molecular details of its mechanism of action on luciferins such as coelenterazine remained elusive. Now, protein crystal structures and biochemical analyses provide an atomistic description of its catalytic mechanism.

    • Andrea Schenkmayerova
    • Martin Toul
    • Martin Marek
    Research
    Nature Catalysis
    Volume: 6, P: 23-38

  • Untargeted mass spectrometry (MS) produces complex, multidimensional data. The MZmine open-source project enables processing of spectral data from various MS platforms, e.g., liquid chromatography–MS, gas chromatography–MS, MS–imaging and ion mobility spectrometry–MS, and is specialized for metabolomics.

    • Steffen Heuckeroth
    • Tito Damiani
    • Tomáš Pluskal
    Protocols
    Nature Protocols
    Volume: 19, P: 2597-2641

  • Feature-based molecular networking is used to analyze non-targeted liquid chromatography–tandem mass spectrometry metabolomics data. This protocol includes instructions, ready-made code and a web app (https://fbmn-statsguide.gnps2.org/) for statistical analysis of feature-based molecular networking results.

    • Abzer K. Pakkir Shah
    • Axel Walter
    • Daniel Petras
    Protocols
    Nature Protocols
    Volume: 20, P: 92-162

  • Feature-based molecular networking allows the generation of molecular networks for mass spectrometry data that can recognize isomers, incorporate relative quantification and integrate ion mobility data.

    • Louis-Félix Nothias
    • Daniel Petras
    • Pieter C. Dorrestein
    Research
    Nature Methods
    Volume: 17, P: 905-908