Analytical Chemistry · 2011 · 336 citations · 0 references
ComputingBioinformaticsVisualizationAnalytical ChemistryData VisualizationMass Spectrometric AnalysisData IntegrationData PipelinesMass SpectrometryMass Spectrometry Data AnalysisMass Spectrometry-based ProteomicsProteomics Data IntegrationArchival File FormatsData Analysis AlgorithmsFile Format ManagementHigh-resolution Mass AnalysisMass Spectral Data AnalysisMass Spectral ProcessingMass Spectrometry Data IntegrationMass Spectrometry-based Annotation
High‑resolution mass spectrometry has produced many analysis methods, but heterogeneous file formats and monolithic software hinder flexible integration, despite mzXML, mzData, and mzML providing uniform raw data access. This work introduces PeakML, a simple yet powerful format for uniform exchange of processed and result data in mass spectrometry. An open‑source Java toolkit (mzMatch) and a visualization environment (PeakML Viewer) were created, demonstrating that PeakML enables flexible data exchange—including integration with XCMS—and gives downstream analyses direct access to full mass trace information for rapid verification. PeakML/mzMatch is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.
The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. In this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.