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Articles by Daniel Petras
Bridging complexity and accessibility in metabolomics with MetaboApps
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 processing and analysis workflows used, many of which require advanced computational expertise.
ENVnet provides a global molecular resource of dissolved organic matter
Abstract Dissolved organic matter (DOM) is a central component of Earth’s carbon cycle and one of the planet’s most chemically diverse pools, yet the molecular structures of its constituents remain largely unresolved. This limitation has hindered our ability to link DOM composition to microbial processes and ecosystem function.
Structure-centric searching enables global mapping of the public metabolome
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Abstract Searching and learning from aggregated public metabolomics data spanning thousands of studies remained largely inaccessible. Here we present StructureMASST, a web-based application enabling scalable, structure-centric searches across public metabolomics repositories using molecule names or chemical representations.
By Yasin El Abiead, Vincent Charron-Lamoureux, Michael Ströbel, Haoqi Zhao, Kine Eide Kvitne, Simone Zuffa, Helena Mannochio-Russo, Harsha Gouda, Cristina Bez, Abubaker Patan, Shipei Xing, Jasmine Zemlin, Julius Agongo, Lindsey A. Burnett, Jarmo-Charles J Kalinski, Daniel Petras, Nikiforos A. Alygizakis, Jeremy J Carver, Thomas H Payne, Eoin Fahy, Shankar Subramaniam, Juan Antonio Vizcaino, Mingxun Wang, Pieter C. Dorrestein, Ipsita Mohany, Victoria Deleray, Abzer K. Pakkir Shah, Ozgur Yurekten
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Nature
Verified
Widespread presence of anthropogenic compounds in marine dissolved organic matter
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Abstract Chemical pollution has profound impacts on marine ecosystem health and services. Most investigations of the distributions of anthropogenic organic chemicals (xenobiotics) have been regionally focused, which limits our understanding of the extent of chemical pollution in the world’s largest biome. To address this gap, we mapped the presence of xenobiotics across marine ecosystems.
By Jarmo-Charles J Kalinski, Shane Farrell, Lisa Schellenberg, Lana G. Graves, Tilman Schramm, Paolo Stincone, Irina Koester, Brandon Stephens, Ralph Torres, Lucia Cancelada, Caroline Utermann-Thüsing, Zachary A. Quinlan, Linda Kelly, Craig Carlson, Cristóbal Castillo-Ilabaca, Silvio Pantoja-Gutiérrez, J. Michael Beman, Aaron C. Hartmann, Allegra T. Aron, Xavier Siwe Noundou, Rosemary A. Dorrington, Deniz Tasdemir, Andreas F. Haas, Pieter C. Dorrestein, Craig Nelson, Lihini I. Aluwihare, Mingxun Wang, Daniel Petras
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Nature
Verified
Tropical cyclones drive oxygen minimum zone shoaling and simultaneously alter organic matter production
Abstract Tropical cyclones regularly form above the ocean’s largest subsurface oxygen minimum zone (OMZ) in the eastern tropical North Pacific Ocean (ETNP), yet how these powerful storms affect this biogeochemically important region remains unknown. We captured multiple direct and potentially interactive oceanographic effects of a Category 4 hurricane (Bud) during a 2018 research cruise in the ETNP.
Turf algae redefine the chemical landscape of temperate reefs, limiting kelp forest recovery
Editor’s summary Kelp creates dense underwater forests in coastal temperate waters, providing habitat for numerous ecologically and economically important animals. Recently, kelp forests in warming waters have been replaced by qualitatively different beds of red algae. “Turf algae” appear to prevent kelp recovery, creating an alternative stable state. Farrell et al.
Oxidation state of bioavailable dissolved organic matter influences bacterioplankton respiration and growth efficiency - Communications Biology
Abstract Oxygen consumption by oceanic microbes can predict respiration (CO2 production) but requires an assumed respiratory quotient (RQ; ΔO2/ΔCO2). Measured apparent RQs (ARQs) can be impacted by various processes, including nitrification and changes in dissolved organic matter (DOM) composition, leading to discrepancies between ARQ and actual RQ.
Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic state
Abstract Simultaneous measurements of library barcodes and metabolites can facilitate the screening of metabolically engineered bacterial libraries. Here, we introduce a scalable method for the parallel measurement of protein-based library barcodes and metabolites using flow-injection mass spectrometry (FI-MS). Protein barcodes are based on ubiquitin, a small 76-amino-acid protein, which we labeled with N-terminal tags of six amino acids to identify bacterial strains.
Reproducible mass spectrometry data processing and compound annotation in MZmine 3 - Nature Protocols
Abstract Untargeted mass spectrometry (MS) experiments produce complex, multidimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and convert it into a more comprehensible format. Depending on the sample type and/or goal of the study, a variety of MS platforms can be used for such analysis.
The redox-sensitive R-loop of the carbon control protein SbtB contributes to the regulation of the cyanobacterial CCM - Scientific Reports
Abstract SbtB is a PII-like protein that regulates the carbon-concentrating mechanism (CCM) in cyanobacteria. SbtB proteins can bind many adenyl nucleotides and possess a characteristic C-terminal redox sensitive loop (R-loop) that forms a disulfide bridge in response to the diurnal state of the cell. SbtBs also possess an ATPase/ADPase activity that is modulated by the redox-state of the R-loop. To investigate the R-loop in the cyanobacterium Synechocystis sp.
Venomics and Peptidomics of Palearctic vipers: Clade-wide analysis of seven taxa of the genera Vipera, Montivipera, Macrovipera and Daboia across Türkiye
Abstract Snake venom variations are a crucial factor to understand the consequences of snakebite envenoming worldwide and therefore it's important to know about toxin composition alterations between taxa. Palearctic vipers of the genera Vipera, Montivipera, Macrovipera and Daboia have high medical impacts across the Old World. One hotspot for their occurrence and diversity is Türkiye on the border between the continents, but many of their venoms remain still understudied.
Venomics and Peptidomics of Palearctic Vipers: A Clade-Wide Analysis of Seven Taxa of the Genera Vipera, Montivipera, Macrovipera, and Daboia across Türkiye
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Proteome Res. 2024, XXXX, XXX RETURN TO ARTICLES ASAPPREVArticleNEXT * Maik Damm Institut für Chemie, Technische Universität Berlin, Straße des 17.
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics - Nature Communications
Abstract Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments.
Publisher Correction: Progress and challenges in exploring aquatic microbial communities using non-targeted metabolomics - The ISME Journal
Correction to: The ISME Journal https://doi.org/10.1038/s41396-023-01532-8, published online 19 October 2023 Unfortunately, there was a mix-up in the numbering of references and reference titles during typesetting between the proofs and the published article. The moved references have been listed below and the correct reference numbers and corrected titles for two references are provided.
High Resolution Biological and Physical Sampling Reveals Expression of Domoic Acid Biosynthetic Genes at Frontal Zones
Abstract Ocean microbes are the foundation of marine food webs, regulating carbon cycling and ecosystem dynamics. How they proliferate, die, move, and interact is regulated by physical, chemical, and biological factors that are dynamic and challenging to quantify in the natural environment. A significant limitation in many marine field studies is the inability to continuously sample the ever-changing ocean environment over space and time.
Progress and challenges in exploring aquatic microbial communities using non-targeted metabolomics - The ISME Journal
Abstract Advances in bioanalytical technologies are constantly expanding our insights into complex ecosystems. Here, we highlight strategies and applications that make use of non-targeted metabolomics methods in aquatic chemical ecology research and discuss opportunities and remaining challenges of mass spectrometry-based methods to broaden our understanding of environmental systems.
Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses - Communications Biology
Abstract The dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, Oʻahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts.
Portosystemic shunt placement reveals blood signatures for the development of hepatic encephalopathy through mass spectrometry - Nature Communications
Abstract Elective transjugular intrahepatic portosystemic shunt (TIPS) placement can worsen cognitive dysfunction in hepatic encephalopathy (HE) patients due to toxins, including possible microbial metabolites, entering the systemic circulation. We conducted untargeted metabolomics on a prospective cohort of 22 patients with cirrhosis undergoing elective TIPS placement and followed them up to one year post TIPS for HE development.
Metabolites | Free Full-Text | ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction
Open AccessArticle by Zachary A. Quinlan 1,*, Irina Koester 1, Allegra T. Aron 2,3, Daniel Petras 4, Lihini I. Aluwihare 1, Pieter C. Dorrestein 3, Craig E.
A Universal Language for Finding Mass Spectrometry Data Patterns
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Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment
Abstract Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes.
Feature-based molecular networking in the GNPS analysis environment
Abstract Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry. Fig.
Reproducible molecular networking of untargeted mass spectrometry data using GNPS
Abstract Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule–focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user’s underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale.
Mass spectrometry searches using MASST - Nature Biotechnology
To the Editor — We introduce a web-enabled mass spectrometry (MS) search engine, named Mass Spectrometry Search Tool (MASST; https://masst.ucsd.edu). By enabling searches of all small-molecule tandem MS (MS/MS) data in public metabolomics repositories, we posit that MASST will unlock these resources for clinical, environmental and natural product applications. MASST can be used in several ways for research questions, which are detailed here.
Feature-based Molecular Networking in the GNPS Analysis Environment
New Results View ORCID ProfileLouis Felix Nothias, View ORCID ProfileDaniel Petras, View ORCID ProfileRobin Schmid, View ORCID ProfileKai Dührkop, View ORCID ProfileJohannes Rainer, Abinesh Sarvepalli, Ivan Protsyuk, View ORCID ProfileMadeleine Ernst, View ORCID ProfileHiroshi Tsugawa, Markus Fleischauer, Fabian Aicheler, View ORCID ProfileAlexander Aksenov, Oliver Alka, View ORCID ProfilePierre-Marie Allard, Aiko Barsch, Xavier Cachet, Mauricio Caraballo, View ORCID ProfileRicardo R.
Tundrenone: An Atypical Secondary Metabolite from Bacteria with Highly Restricted Primary Metabolism
Methane-oxidizing bacteria, aerobes that utilize methane as their sole carbon and energy source, are being increasingly studied for their environmentally significant ability to remove methane from the atmosphere. Their genomes indicate that they also have a robust and unusual secondary metabolism.
Significance estimation for large scale metabolomics annotations by spectral matching
Our first method that we assessed uses an empirical Bayes approach24 whereas the second, third and fourth FDR estimation methods rely on the target-decoy approach, using different decoy databases (Fig. 1a–d). Although the generation of “random” MS/MS spectra for small molecules is conceptually more challenging than for peptides25, it became possible with recent methodological advances9, 26,27,28.
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