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

Background: 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. Results: 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 isotop...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Tomás Pluskal, Sandra Castillo, Alejandro Villar-Briones, Matej Oresic
• Keywords: BMCBI 2010, Data Processing, Mass Spectrometry, Quantitative Profiling