Reproducibility and robustness are essential to any research endeavor but are particularly important when studying something as complex and dynamic as the proteome. Researchers and institutions make large investments in experiments studying biology at proteome scale. They expect data generated from proteomics experiments will be robust enough to guide future research efforts. This data must hold from study to study and be reproducible from institution to institution. Only with the confidence that such reproducibility inspires can researchers efficiently move forward with biomarker and drug development efforts.
The NautilusTM Proteome Analysis Platform was conceived with reproducibility and robustness at its core. Its underlying method, Iterative Mapping, is designed to consistently generate high quality data, and we cover some of the key factors designed to enable its reproducibility here.
Key characteristics designed to make Iterative Mapping reproducible
Intact, single-molecule protein counting driven by many probe binding events
In Iterative Mapping, billions of full-length proteins are isolated and identified at the single-molecule level using probes designed to bind features indicative of protein or proteoform identity. Unlike standard methods that identify proteins or proteoforms through a small number of detection events (think 1-2 antibody binding interactions in standard affinity methods or the handful peptides detected per protein in mass spec), we aim for Iterative Mapping to identify most proteins and proteoforms through many binding events. In fact, for broadscale proteomics analyses quantifying all proteins in the proteome, Iterative Mapping is designed to identify most proteins with more than 30 probe binding events. In targeted proteoform analyses, we probe each molecule multiple times with every proteoform feature-targeting reagent to ensure we have high confidence in the features detected.
Once all molecules are identified, they are quantified by summing all those identified as the same proteins or proteoforms. Quantifications come from the precise and direct counting of individual molecules. Ultimately, single-molecule detection = quantification, and we intend to provide researchers with easy-to-understand readouts of digital protein counts.
Standardized single-molecule protein library preparation and instrument automation
As part of our platform’s standard workflow, we aim to provide kits for single-molecule protein library preparation from customer samples. These will be designed to make the library preparation process as simple and straightforward as possible. Once such protein libraries are generated, they will be loaded onto the platform where automated robotics will handle the rest. With this hands-off and standardized approach, we aim to further ensure reproducibility.
Solving frustrations with traditional proteomic analyses
We designed the Nautilus Proteome Analysis Platform with a keen awareness of researcher’s frustrations with proteomics tools today. Researchers consistently tell us that traditional proteomic analysis workflows are too technically demanding and deliver unreliable data. From sample preparation to results, we have designed our workflows to be as simple and straightforward as possible. Thus, our platform is designed to solve researchers’ frustrations directly and provide reproducible and robust results of the highest caliber.
For a clear look at the reproducible data generated by Iterative Mapping, be sure to read our preprint where we quantified 130 tau proteoforms with <6% CVs over many potential sources of variability.
Learn how you can incorporate Iterative Mapping into your workflows.
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