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
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Host affinity of endophytic fungi and the potential for reciprocal interactions involving host secondary chemistry.
Natalie Christian,Natalie Christian,Brian E. Sedio,Brian E. Sedio,Ximena Florez‐Buitrago,Luis A. Ramírez-Camejo,Enith I. Rojas,Luis C. Mejía,Sage Palmedo,Autumn Rose,John W. Schroeder,John W. Schroeder,Edward Allen Herre +12 more
TL;DR: The results suggest at least two potential processes: (1) Plant secondary chemistry influences assembly and composition of fungal endophytic communities, and (2) host colonization by endophytes subsequently induces changes in the host chemical landscape.
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KPIC2: An Effective Framework for Mass Spectrometry-Based Metabolomics Using Pure Ion Chromatograms
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Onur Erbilgin,Oliver Ruebel,Katherine B. Louie,Matthew Trinh,Markus de Raad,Tony Wildish,Daniel W. Udwary,Cindi A. Hoover,Samuel Deutsch,Trent R. Northen,Benjamin P. Bowen +10 more
TL;DR: The findings suggest that coupling metabolomics and genomics data by scoring consensus between the two increases the quality of both metabolite identifications and gene annotations in this organism, and also provides testable hypotheses for specific biochemical functions.
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