Modern proteomics experiments generate vast amounts of data. Manual analysis and management of this data requires an inordinate amount of time from researchers and bioinformaticians. Furthermore, when methods of data analysis and management are customized for individual labs, it quickly becomes difficult to share data between institutions or provide traceability and reproducibility, and a bottleneck quickly forms around analysis and the ability to derive meaningful results from data. We present an automated and integrated pipeline of software tools to address the data analysis and management needs of modern proteomics facilities. By integrating previously stand-alone point analysis tools, an open spectra viewer, and a proteomics lab information and data management solution, we provide a Trans Proteomic Pipeline to analyze, manage and share proteomics data.

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