Millisecond Informatics in Action

Recent developments in intelligent data acquisition strategies are leading the next generation of multiplexed proteome quantitation. Real-time peptide spectral matching enables superior quantitation and speed compared to canonical methods. Intelligent data acquisition strategies require millisecond time-scale informatics pipelines for real time decision making. These included spectral pre-processing, analysis, peptide spectral matching, and false discovery rate estimation for spectral filtering. In this work we present a first-of-its-kind, fast and robust informatics workflow that is capable of assigning peptide-level false discovery rates on a millisecond time scale with high fidelity to offline statistical methods. The millisecond informatics pipeline, Orbiter, was built in C# to support interfacing with the Thermo Fusion API for online instrument control. We applied the real-time search module within the Orbiter pipeline to analyze large sample cohorts in half the time as previously needed for canonical analyses. We used these more efficient analytical workflows to profile murine aging across ten tissues. Covering 200 samples and more than 11,000 proteins in just 18 days, RTS enabled the determination of quantitative profiles indicative of age-based protein changes in kidney, adipose tissue, and murine brain regions.