Aptamer Sequencing for Accurate Multiplex Protein Quantification
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Solution Overview
Problem
Current proteomics techniques face challenges in accurately and efficiently quantifying proteins in complex mixtures, particularly in biological samples like blood, due to the wide range of protein concentrations and the limitations of Mass Spectrometry-based methods, which often result in incomplete resolution and unreliable identification of peptides, and the high cost and time-consuming nature of antibody-based validation processes.
Innovation Solution
The use of aptamers as molecular tags, combined with next-generation polynucleotide sequencing, allows for direct quantification of proteins by sequencing the aptamer sequences after binding to proteins, minimizing sample manipulation and enabling simultaneous quantification of multiple proteins in a single assay.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If Mass Spectrometry-based methods are used for protein quantification, then protein identification capability is provided, but measurement precision and reliability deteriorate due to wide concentration ranges and incomplete peptide resolution
Solution Approach 1:
The patent introduces aptamers as intermediary molecules that bind to target proteins and serve as mediators for quantification. These aptamers act as bridges between the protein of interest and the detection system, enabling accurate measurement without directly analyzing the complex protein mixture through Mass Spectrometry, thereby resolving the contradiction between quantification accuracy and identification reliability
Solution Approach 2:
The patent creates a copy of the protein quantification problem by using aptamer sequences as proxies. Instead of directly measuring proteins through MS, the system sequences the aptamer copies that bound to proteins, converting a difficult protein analysis problem into a more reliable nucleotide sequencing problem, thus improving both measurement precision and reliability
2Reliability
If antibody-based validation processes are used, then protein validation is achieved, but time consumption and cost increase significantly
Solution Approach 1:
The patent replaces the complex, time-consuming antibody-based validation system with a streamlined aptamer sequencing system. By substituting the mechanical and biochemical complexity of antibody production and validation with a more direct nucleotide sequencing approach, the system achieves comparable or superior validation reliability while dramatically reducing time and cost
Solution Approach 2:
The patent changes the fundamental parameter of validation from antibody binding affinity measurement to aptamer sequence identification. This parameter change transforms the validation process from a complex biochemical assay to a more straightforward sequencing task, reducing both time consumption and cost while maintaining reliability
3Measurement precision
If selective purification methods are used to exclude high-abundance proteins, then low-abundance protein detection is improved, but process complexity and time consumption increase
Solution Approach 1:
The patent creates a universal aptamer-based detection system that can simultaneously handle both high-abundance and low-abundance proteins without requiring separate purification steps. The aptamers specifically bind to target proteins of interest regardless of the background complexity, providing a multi-functional solution that simplifies the overall process while maintaining detection precision
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This method provides a more sensitive, efficient, and cost-effective means of quantifying proteins, allowing for high-throughput analysis and reducing the time and cost associated with biomarker discovery and validation, while maintaining the proteins in their native configuration.
Implementation Method 1
combining the sample, or a derivative thereof, with one or more aptamers and allowing one or more molecules in the sample to bind to the aptamer(s)
Implementation Method 2
quantification of the bound molecule(s) is carried out by sequencing at least part of the or each aptamer
Data Source
AI summary
The present invention is a method for measuring the amount of at least one molecule in a biological sample, the method comprising a) combining the sample, or a derivative thereof, with one or more aptamers and allowing one or more molecules in the sample to bind to the aptamer(s); b) separating bound from unbound molecules; and c) quantifying the molecule(s) bound to the or each aptamer, wherein quantification of the bound molecule(s) is carried out by sequencing at least part of the or each aptamer. Uses of and products derived from the method are also contemplated.