TOPPAS: A Graphical Workflow Editor for the Analysis of High-Throughput Proteomics Data
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- 作者：Johannes Junker ; Chris Bielow ; Andreas Bertsch ; Marc Sturm ; Knut Reinert ; Oliver Kohlbacher
- 刊名：Journal of Proteome Research
- 出版年：2012
- 出版时间：July 6, 2012
- 年：2012
- 卷：11
- 期：7
- 页码：3914-3920
- 全文大小：369K
- 年卷期：v.11,no.7(July 6, 2012)
- ISSN：1535-3907
文摘
Mass spectrometry coupled to high-performance liquid chromatography (HPLC鈥揗S) is evolving more quickly than ever. A wide range of different instrument types and experimental setups are commonly used. Modern instruments acquire huge amounts of data, thus requiring tools for an efficient and automated data analysis. Most existing software for analyzing HPLC鈥揗S data is monolithic and tailored toward a specific application. A more flexible alternative consists of pipeline-based tool kits allowing the construction of custom analysis workflows from small building blocks, e.g., the Trans Proteomics Pipeline (TPP) or The OpenMS Proteomics Pipeline (TOPP). One drawback, however, is the hurdle of setting up complex workflows using command line tools. We present TOPPAS, The OpenMS Proteomics Pipeline ASsistant, a graphical user interface (GUI) for rapid composition of HPLC鈥揗S analysis workflows. Workflow construction reduces to simple drag-and-drop of analysis tools and adding connections in between. Integration of external tools into these workflows is possible as well. Once workflows have been developed, they can be deployed in other workflow management systems or batch processing systems in a fully automated fashion. The implementation is portable and has been tested under Windows, Mac OS X, and Linux. TOPPAS is open-source software and available free of charge at http://www.OpenMS.de/TOPPAS.