A cross-platform toolkit for mass spectrometry and proteomics

MC Chambers, B Maclean, R Burke, D Amodei… - Nature …, 2012 - nature.com
MC Chambers, B Maclean, R Burke, D Amodei, DL Ruderman, S Neumann, L Gatto
Nature biotechnology, 2012nature.com
for processing and analyzing complex proteomics data sets in a platform-agnostic manner
has become critical. With version 3.0 of the ProteoWizard Toolkit8, we attempt to mitigate
these challenges through open-source, permissively licensed, cross-platform software. The
Toolkit has two components: first, a suite of libraries that facilitate the development and
comparison of tools for proteomics data analysis; and second, a set of tools, developed
using these libraries, that performs a wide array of common proteomics analyses. The …
for processing and analyzing complex proteomics data sets in a platform-agnostic manner has become critical. With version 3.0 of the ProteoWizard Toolkit8, we attempt to mitigate these challenges through open-source, permissively licensed, cross-platform software. The Toolkit has two components: first, a suite of libraries that facilitate the development and comparison of tools for proteomics data analysis; and second, a set of tools, developed using these libraries, that performs a wide array of common proteomics analyses. The Toolkit has been developed under modern design principles in the C++ language and supports a variety of platforms with native compilers (GCC on Linux, MSVC on Windows and XCode on OSX). The toolkit was released under the Apache 2.0 license10 to ensure that it can be used in both academic and commercial projects. New to ProteoWizard 3.0 and unlike previous efforts, vendor reader libraries are now directly distributed with the Toolkit independently of instrument control libraries (a further description of new features can be found in Supplementary Text 1). Furthermore, ProteoWizard employs a single converter and access interface for all formats; this singular point of maintenance allows a more stable and optimized set of tools. Additional robustness comes from ProteoWizard’s use of a continuous integration and testing environment. Although common in commercial projects, this scale of quality assurance is uncommon in traditional academic projects.
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