A High-Throughput Bioinformatics Platform for Mass Spectrometry-Based Proteomics

The success of mass spectrometry-based proteomics in emerging applications such as biomarker discovery and clinical diagnostics, is predicated substantially on its ability to achieve growing demands for throughput. Support for high throughput implies sophisticated tracking of experiments and the experimental steps, larger amounts of data to be organized and summarized, more complex algorithms for inferring and tracking protein expression across multiple experiments, statistical methods to access data quality, and a streamlined proteomics-centric bioinformatics environment to establish the biological context and relevance of the experimental measurements. This paper presents a bioinformatics platform that was built for an industrial mass spectrometry-based proteomics laboratory focusing on biomarker discovery. The basis of the platform is a robust and scalable information management environment supported by database and workflow management technology that is employed for the integration of heterogeneous data, applications and processes across the entire laboratory workflow. This paper focuses on selected features of the platform which include: (a) a method for improving the accuracy of protein assignment, (b) novel software tools for protein expression analysis that combine differential MS quantitation with tandem MS for peptide identification, and (c) integration of methods to aid the biological relevance and statistical significance of differentially expressed proteins.