PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis

摘要

ABSTRACT: The recent proliferation of high-resolution massnspectrometers has generated a wealth of new data analysisnmethods. However, flexible integration of these methods intonconfigurations best suited to the research question is hamperednby heterogeneous file formats and monolithic software develop-nment. The mzXML, mzData, and mzML file formats havenenabled uniform access to unprocessed raw data. In this papernwe present our efforts to produce an equally simple and powerfulnformat, PeakML, to uniformly exchange processed intermediarynand result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, andnannotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakMLnViewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groupsnor companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch datanprocessing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace informationnunderlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatchnsoftware is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.