Improving Laboratory Performance and Discovery with BioAnalyte Solutions
The Food and Drug Administration’s (FDA) Center for Food Safety and Applied Nutrition (CFSAN) has coordinated many of the activities of the Food Safety Initiative (FSI) since its inception in 1998. CFSAN's comprehensive and active core research program and its FSI-supported research efforts play major roles in achieving the goal of reducing levels of food borne illness in the United States. They help maintain the Agency's awareness of emerging issues, and they enable the Agency to rapidly respond to emergency situations. FSI research activities focus in particular on those hazards that contribute most significantly to the estimated 76 million food-borne illness and 5,000 deaths which occur within the United States each year.
The Problem – Rapid Identification of Strains of Bacteria
The FDA’s CFSAN is tasked with developing methods of characterizing new strains of bacteria as they arise in the food chain. However, the state of the art in microbiology didn’t have the specificity to precisely indicate when a new potentially dangerous strain had evolved. Furthermore, the protein-based methods that did exist required weeks of manual effort to get results. The FDA needed a solution to rapidly identify new strains while automating the process. Steve Musser and John Callahan, Research Chemists, searched for LC/MS data analysis software that would address these challenges. They found LC/MS software packages that solved only parts of the challenge; however, there was no integrated ‘whole solution’. Then they discovered BioAnalyte where all of the tools resided under one roof. Under their guidance, BioAnalyte developed both ProTrawler and Regatta.
The Solution – BioAnalyte’s Regatta Solves the Seemingly Intractable Problems
ProTrawler and Regatta presented the first integrated software package that provided whole solution for the Musser / Callahan laboratory. Previously, it would take weeks to do the analysis ‘by hand’ using instrument vendor-supplied software. With the initial implementation of ProTrawler, the time it took to complete the data analysis for experiment went from weeks to hours. The FDA benefited from features such as 100x deconvolution speed improvement, better error estimates, and process automation. With the current version of ProTrawler, they further improved productivity and now accomplish the experiment in one hour – a remarkable achievement. Indeed, the FDA can now process days worth of data faster than it takes to acquire the data, eliminating the data analysis bottleneck altogether. The performance improvements afford them the luxury of doing multiple runs of a single sample, providing them with a detailed protein expression signature of bacterium in only an hour. With ProTrawler’s complimentary solution, Regatta, which is designed for comparative analysis of LC/MS data, the sample data can be easily compared, contrasted, and worked over in fine multivariate detail.
The Result – Unprecedented ROI and Lab Results
For the FDA, BioAnalyte solutions have opened up an entirely new area of experimentation. It’s been a quantum leap in productivity. The FDA experienced significant improvements in their lab processes and results. They were able to improve experiment turnaround times that typically took three weeks to perform to in hours. The cost savings to the FDA have been in the hundreds of thousands of dollars. Callahan sees a bright future for ProTrawler and Regatta. One of the most promising applications is the emerging field of ‘Intact Protein’ mass spectrometry as it is faster, more reproducible, and more accurate than two-dimensional gel electrophoresis. Intact Protein MS also has great potential as a complement to ‘Bottom-Up’ Proteomics because it predicts which proteins and protein sequences are relevant for research goals.