Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.
BACKGROUND
In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size.


RESULTS
Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data.


BACKGROUND
Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS.
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland; Ph.D. Program in Systems Biology, University of Zurich and ETH Zurich, CH-8057 Zurich, Switzerland.
Hannes L
HL
Röst
ID Scientific IT Services, ETH Zurich, CH-8092 Zurich, Switzerland.
Uwe
U
Schmitt
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland; Competence Center for Systems Physiology and Metabolic Diseases, CH-8093 Zurich, Switzerland; Faculty of Science, University of Zurich, CH-8057 Zurich, Switzerland.
Ruedi
R
Aebersold
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland; S3IT, University of Zurich, CH-8057 Zurich, Switzerland.
Lars
L
Malmström
D000465:Algorithms; D030562:Databases, Protein; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*