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Next Generation Protein SequencingTM is opening up in-depth exploration of the proteome similar to how next-generation DNA sequencing resulted in advancing our understanding of the genome and transcriptome. However, unlike genes, proteins are far more complex due to their variants and modifications, resulting in over a million different proteoforms that directly influence human health and disease.
It is no surprise that 85% of the human proteome is undruggable, presenting a significant opportunity to identify and characterize the role proteins play in human health and disease.1
Traditional methods for detecting proteins do not provide amino acid–level sequencing information in an easy-to-interpret and accessible workflow. They certainly yield valuable information but often do not recognize important protein variants and modifications at the amino acid level. Quantum-Si’s first-of-its-kind Platinum™ next-generation protein sequencing instrument and user-friendly workflow enable single-molecule resolution to facilitate protein identification from biological samples.
Enabling Proteomics
Platinum utilizes dye-tagged N-terminal amino acid recognizers and semiconductor chip technology to detect both the binding characteristics and binding order of N-terminal amino acids, resulting in unique kinetic signatures that can be used to differentiate and identify amino acid residues and their modifications. A practical choice for a wide range of labs, the convenient, accessible benchtop instrument and easy-to-use interface eliminates the need for specialized expertise to operate equipment or interpret data. Cloud-based software converts kinetic signatures into meaningful protein identification.
A New Approach to Protein Identification
A common workflow for studying proteins from biological samples is immunoprecipitation (IP) to enrich and concentrate proteins of interest. IP uses an antibody followed by a detection method such as western blot using the same primary antibody.
Platinum simplifies the overall workflow. Quantum-Si’s team demonstrated the ability to use only one antibody to perform IP and enrich IL-6 from human serum followed by protein identification of IL-6 using Platinum next-generation protein sequencing. While still attached to the bead and antibody, the isolated proteins were digested into peptide fragments and attached to macromolecular linkers at the C-terminus. Next, the peptides were immobilized on the semiconductor chip, and the standard Platinum protein sequencing workflow was applied.
Non-antibody-based approaches are also desirable to distinguish differences in amino acid sequences and isoforms of similar size, especially if specific antibodies are not available for detection. An in-gel protein digestion method was shown to be compatible with Quantum-Si’s library preparation and protein sequencing workflows. The method can be used for the separation and enrichment of single proteins from complex mixtures using SDS-PAGE, followed by protein extraction, library preparation, and protein identification on Platinum. The method has the potential to facilitate the preseparation and identification of multiple proteins from complex protein mixtures and to identify proteins from bands on a gel.
Range of Applications
In addition, Platinum can be used to discern between different protein variants. For example, the information-rich output from next-generation protein sequencing allows for the identification and distinction between the unique protein sequences of the three main SARS-CoV-2 variants, Alpha, Delta, and Omicron. This ability to directly distinguish amino acid variants and modifications provides researchers with a tool to understand biomarkers in greater detail.
The importance of single amino acid variant and modification detection and the possibilities it holds for future applications in disease and biomarker discovery is enormous and cannot be dismissed. Having a convenient, accessible technology such as Platinum that is able to use kinetic signatures to directly detect variances in amino acid sequence at single-molecule resolution unlocks the door to new applications that have the potential to provide new insights that increase the knowledge of how proteins impact human health and disease. Finally, a tool is within reach that enables everyone access to critical protein sequence data to aid in the understanding and harnessing of the proteome.
Reference
- Spradlin JN, Zhang E, Nomura DK. Reimagining Druggability Using Chemoproteomic Platforms. Acc Chem Res. 2021 Apr 6; 54(7): 1801–1813. DOI: 10.1021/acs. accounts.1c00065.
Learn more about the Platinum™ Next-Generation Protein Sequencer www.quantum-si.com
