MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
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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MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis.
Jasmine Chong,Othman Soufan,Carin Li,Iurie Caraus,Shuzhao Li,Guillaume Bourque,David S. Wishart,Jianguo Xia +7 more
TL;DR: The user interface of MetaboAnalyst 4.0 has been reengineered to provide a more modern look and feel, as well as to give more space and flexibility to introduce new functions.
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MetaboAnalyst 3.0—making metabolomics more meaningful
TL;DR: By completely re-implementing the MetaboAnalyst suite using the latest web framework technologies, the server has been able to substantially improve its performance, capacity and user interactivity.
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The re-emergence of natural products for drug discovery in the genomics era
TL;DR: This work reviews strategies for natural product screening that harness the recent technical advances that have reduced technical barriers and assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products.
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Discovery and resupply of pharmacologically active plant-derived natural products: A review.
Atanas G. Atanasov,Birgit Waltenberger,Eva-Maria Pferschy-Wenzig,Thomas Linder,Christoph Wawrosch,Pavel Uhrin,Veronika Temml,Limei Wang,Stefan Schwaiger,Elke H. Heiss,Judith M. Rollinger,Judith M. Rollinger,Daniela Schuster,Johannes M. Breuss,Valery N. Bochkov,Marko D. Mihovilovic,Brigitte Kopp,Rudolf Bauer,Verena M. Dirsch,Hermann Stuppner +19 more
TL;DR: While the intrinsic complexity of natural product-based drug discovery necessitates highly integrated interdisciplinary approaches, the reviewed scientific developments, recent technological advances, and research trends clearly indicate that natural products will be among the most important sources of new drugs in the future.
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MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights.
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TL;DR: The MetaboAnalyst 5.0 as mentioned in this paper is the latest version of the web-based platform for comprehensive metabolomics data analysis and interpretation, aiming to narrow the gap from raw data to functional insights for global metabolomics based on HRMS.
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