MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
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TLDR
A new generation of a popular open-source data processing toolbox, MZmine 2 is introduced, suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.Abstract:
Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2. A key concept of the MZmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. Data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. Newly introduced functionality includes the identification of peaks using online databases, MSn data support, improved isotope pattern support, scatter plot visualization, and a new method for peak list alignment based on the random sample consensus (RANSAC) algorithm. The performance of the RANSAC alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms. MZmine 2 is freely available under a GNU GPL license and can be obtained from the project website at: http://mzmine.sourceforge.net/
. The current version of MZmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.read more
Citations
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Discovery of sustainable drugs for neglected tropical diseases: cashew nut shell liquid (CNSL)-based hybrids target mitochondrial function and ATP production in Trypanosoma brucei
Michela Cerone,Michela Cerone,Elisa Uliassi,Federica Prati,Godwin U. Ebiloma,Godwin U. Ebiloma,Leandro Lemgruber,Christian Bergamini,David G. Watson,Thais de A. M. Ferreira,Gabriella Simões Heyn Roth Cardoso,Luiz Antonio Soares Romeiro,Harry P. de Koning,Maria Laura Bolognesi +13 more
TL;DR: Hybrid compounds developed by merging the structural features of quinone 4 (2‐phenoxynaphthalene‐1,4‐dione) with those of phenolic constituents from cashew nut shell liquid (CNSL) might be promising bio‐based sustainable hits for anti‐trypanosomatid drug discovery.
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In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics.
TL;DR: Virtual Metabolomics Mass Spectrometer (ViMMS), a metabolomics LC-MS/MS simulator framework that allows for scan-level control of the MS2 acquisition process in silico, is introduced and shown how ViMMS can be used to optimize N for Top-N data-dependent acquisition (DDA) acquisition, giving results comparable to modifying N on the mass spectrometer.
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Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
Justin P. Shaffer,Louis-Félix Nothias,Luke R. Thompson,Jon G. Sanders,Rodolfo A. Salido,Sneha P. Couvillion,Asker Daniel Brejnrod,Franck Lejzerowicz,Niina Haiminen,Shih-Cheng Huang,Holly L. Lutz,Qiyun Zhu,Cameron Martino,James T. Morton,Smruthi Karthikeyan,Mélissa Nothias-Esposito,Kai Dührkop,Sebastian Böcker,Hyun-Woo Kim,Alexander A. Aksenov,Wout Bittremieux,Jeremiah J. Minich,Clarisse Marotz,MacKenzie Bryant,Karenina Sanders,Tara Schwartz,Gregory Humphrey,Yoshiki Vásquez-Baeza,Anupriya Tripathi,Laxmi Parida,Anna Paola Carrieri,Kristen L. Beck,Promi Das,Antonio Gonzalez,Daniel McDonald,Joshua Ladau,Søren Michael Karst,Mads Albertsen,Gail Ackermann,Jeff DeReus,Daniel Petras,James C. Stegen,Se Jin Song,Thomas O. Metz,Austin D. Swafford,Pieter C. Dorrestein,Janet K. Jansson,Jack A. Gilbert,Rob Knight,Lars T. Angenant,Alison M. Berry,Leonora S. Bittleston,Jennifer L. Bowen,Max Chavarría,G. A. Cowan,Daniel L. Distel,Peter R. Girguis,Jaime Huerta-Cepas,Paul R. Jensen,Ling-bo Jiang,Gary M. King,Anton Lavrinienko,Aurora MacRae-Crerar,Thulani P. Makhalanyane,Tapio Mappes,Ezequiel M. Marzinelli,Gregory D. Mayer,Katherine D. McMahon,Jessica L. Metcalf,Sou Miyake,Timothy A. Mousseau,Catalina Murillo-Cruz,David D. Myrold,Brian Palenik,Adrián A. Pinto-Tomás,Dorota L. Porazinska,Jean-Baptiste Ramond,Forest Rowher,Taniya RoyChowdhury,Stuart A. Sandin,Steven K. Schmidt,Henning Seedorf,Ashley Shade,J. Reuben Shipway,Jennifer A. Smith,Frank J. Stewart,Karen Tait,Torsten Thomas,Yael Tarlovsky Tucker,Jana M. U'Ren,Phillip C. Watts,Nicole S. Webster,Jesse R. Zaneveld,Shan Zhang +93 more
TL;DR: The Earth Microbiome Project (EMP) dataset as discussed by the authors provides a set of 880 microbial community samples collected for the EarthMicrobiome project and includes metagenomic and metabolite data.
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Vochysia tucanorum Mart.: an aluminum-accumulating species evidencing calcifuge behavior
Marcelo Claro de Souza,Gustavo Habermann,Cárita Liberato do Amaral,Annylory Lima Rosa,Marcelo Henrique Ongaro Pinheiro,Fernando B. Da Costa +5 more
TL;DR: Due to the high Al accumulation in plants grown on acidic soil, and their inability to survive in calcareous soil, it is concluded that V. tucanorum is an Al-accumulating species with calcifuge behavior.
Posted ContentDOI
Breastmilk-promoted bifidobacteria produce aromatic lactic acids in the infant gut
Martin Frederik Laursen,Mikiyasu Sakanaka,Mikiyasu Sakanaka,Nicole von Burg,Urs M. Mörbe,Daniel Andersen,Janne Marie Moll,Ceyda T. Pekmez,Aymeric Rivollier,Kim F. Michaelsen,Christian Mølgaard,Mads Vendelbo Lind,Lars O. Dragsted,Takane Katayama,Takane Katayama,Henrik Lund Frandsen,Anne Marie Vinggaard,Martin Iain Bahl,Susanne Brix,William W. Agace,William W. Agace,Tine Rask Licht,Henrik Munch Roager,Henrik Munch Roager +23 more
TL;DR: It is demonstrated that breastmilk-promoted Bifidobacterium species convert aromatic amino acids into their respective aromatic lactic acids via a previously unrecognised aromatic lactate dehydrogenase, and suggested that these microbial metabolites may impact immune function in early life.
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