MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

BMC Bioinformatics
Tomáš PluskalMatej Orešič

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 ...Continue Reading

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Jan 3, 2020·The Journal of Clinical Investigation·Sofia KhanLaura L Elo
Dec 19, 2019·Metabolites·Ali RazzaqFozia Saleem
Feb 20, 2020·American Journal of Botany·Natalie ChristianEdward Allen Herre
Dec 25, 2019·Organic Chemistry Frontiers : an International Journal of Organic Chemistry·Roberta TetaAlfonso Mangoni
Apr 2, 2020·Mass Spectrometry Reviews·Thomas Züllig, Harald C Köfeler
Apr 5, 2020·International Journal of Molecular Sciences·Mariangela KosmopoulouEvagelos Gikas
May 7, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Bruna NevesTânia Melo
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