AUTOPILOT: Top Down Instrument Control and Data Analysis

Overview
AUTOPILOT is an integrated software environment developed to address inadequacies that have been present for years in the proteomics community. Data acquisition and post-acquisition processing are traditionally split into two separate software platforms. We reject this operational paradigm and seek to establish a set of tools to capture the full complexity of modern proteome projects, maximizing proteoform-specific identifications to capture the full characterization power of mass spectrometry. AUTOPILOT will coordinate data acquisition, processing and visualization to tightly connect instrument and computational time with the experimental goals of a sample set.

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High-Throughput Data Analysis with NRTDP Galaxy
A cornerstone to the AUTOPILOT suite of tools is the NRTDP Galaxy environment.  Leveraging the Galaxy open-source bioinformatics environment, we have developed a set of top down proteomics tools that allow rapid MS data searching through integration with the Northwestern University Quest computer cluster.  This tool will lower the “barrier to entry” for large scale top down proteomics. For more information, or to request an account, see our resource software page.

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