Rapidly advance quantitative proteomics with a high-throughput SWATH® Acquisition solution
Microflow LC with OptiFlow® Turbo V Source on the TripleTOF® 6600+ System and cloud processing
Alexandra Antonoplis, Christie Hunter
The combination of microflow LC with SWATH Acquisition for accelerating quantitative proteomics studies is becoming increasingly more widespread, due to the improved robustness and throughput obtained relative to the traditional nanoflow LC approach. Previously an investigation was done to characterize the tradeoff between sensitivity and throughput/robustness when switching from nanoflow to microflow for global protein quantitation experiment using SWATH Acquisition.1 It was demonstrated that with only 4x more total protein on column similar results could be achieved with much higher throughput and robustness.
The impact of shortening microflow gradient length on the number of proteins/peptides quantified from a SWATH Acquisition dataset was also studied, providing a good guidance for researchers when selecting the optimal chromatographic strategy for a study.2
Due to these method optimizations, microflow SWATH Acquisition datasets can be generated with high throughput (up to 100 samples per day, depending on the selected gradient length).2 This will put high pressure on the downstream data processing tools and results generation, to keep pace with the generation of datasets. Thus, processing of Omics datasets in the cloud is becoming increasingly important, to handle the speed and scale of today’s industrialized proteomics approaches.
In this work, using fast microflow gradients, a small set of cell lines were studied to further characterize the impact of fast gradients on quantitative accuracy. Data was collected using the OptiFlow Ion Source on the TripleTOF 6600+ System at two different gradient lengths, 20 and 45 mins. Using the tools in the OneOmics™ Suite in SCIEX Cloud, protein quantitation data was compared (Figure 1).