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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Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.
Alexey V. Melnik,Yoshiki Vázquez-Baeza,Alexander A. Aksenov,Embriette R. Hyde,Andrew C. McAvoy,Mingxun Wang,Ricardo Silva,Ivan Protsyuk,Jason V. Wu,Amina Bouslimani,Yan Wei Lim,Tal Luzzatto-Knaan,William Comstock,Robert A. Quinn,Richard J. Wong,Greg Humphrey,Gail Ackermann,Timothy Spivey,Sharon S. Brouha,Nuno Bandeira,Grace Y. Lin,Forest Rohwer,Douglas Conrad,Theodore Alexandrov,Rob Knight,Pieter C. Dorrestein,Neha Garg +26 more
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Optimization of LC-Orbitrap-HRMS acquisition and MZmine 2 data processing for nontarget screening of environmental samples using design of experiments
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Automated chemical fingerprinting of Mexican spirits derived from Agave (tequila and mezcal) using direct-injection electrospray ionisation (DIESI) and low-temperature plasma (LTP) mass spectrometry
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Characterization of chemical compounds susceptible to be extracted from cork by the wine using GC-MS and 1H NMR metabolomic approaches.
Joana Pinto,Ana Sofia Oliveira,Paulo Sávio Lopes,Isabel Roseira,Miguel Cabral,Maria de Lourdes Bastos,Paula Guedes de Pinho +6 more
TL;DR: Preliminary results unveiled the potential for a more efficient selection of cork planks for stoppers production based on the compounds susceptible to be extracted from cork by the wine.
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