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Abstract

Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and quantify the proteins in biological and clinical samples, identify pathways affected by endogenous and exogenous perturbations, and characterize protein complexes. Despite successes, the interpretation of vast proteomics datasets remains a challenge. There have been several calls for improvements and standardization of proteomics data analysis frameworks, as well as for an application-programming interface for proteomics data access,. In response, we have developed the ProteoWizard Toolkit, a robust set of open-source, software libraries and applications designed to facilitate proteomics research. The libraries implement the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats. In addition, diverse software classes enable rapid development of vendor-agnostic proteomics software. Additionally, ProteoWizard projects and applications, building upon the core libraries, are becoming standard tools for enabling significant proteomics inquiries.

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Figures

Figure 1a
Figure 1a
ProteoWizard uses modern design principles to implement a modular framework of many independent libraries grouped in dependency levels with strict interfaces. This allows extensive development at each level while enforcing stability.
Figure 1b
Figure 1b
The data layer presents a unified access interface to mass spectrometry data. The modular framework allows additional readers for diverse file-types to be easily added via plug-in adapter classes. Developers only need interact with the primary interface to access data, agnostic to the details of an input source file.
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