Nucleic Acid Encoding for Multiplexed Protein Analysis
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Solution Overview
Problem
Current proteomics analysis techniques face challenges in multiplexing, minimizing cross-reactivity, and achieving high-throughput and high-parallel characterization of proteins, particularly in identifying and quantifying post-translational modifications, due to limitations in immunoassay platforms and mass spectrometry methods.
Innovation Solution
A method involving sequential or simultaneous binding of macromolecules with multiple coding-tagged binding agents, transferring identifying information to recording tags, and analyzing these extended tags to achieve high-throughput and high-parallel macromolecule analysis, using nucleic acid encoding for enhanced specificity and sensitivity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If immunoassay platforms are used for protein analysis, then sensitivity and specificity are improved, but multiplexing capability and throughput are limited
Solution Approach 1:
The invention segments the protein analysis process into multiple independent binding cycles, where each cycle uses a different binding agent with a unique coding tag. This allows sequential analysis of multiple proteins or modifications without cross-reactivity, thereby improving multiplexing capability while maintaining the sensitivity and specificity of individual immunoassays.
Solution Approach 2:
The invention introduces coding tags (nucleic acid sequences) as intermediaries that link binding agents to detectable signals. These coding tags serve as mediators that enable high-throughput identification and multiplexing by allowing parallel processing and automated sequencing readout, thus improving throughput while preserving the analytical precision of the original binding events.
2Productivity
If mass spectrometry methods are used for protein characterization, then throughput is improved, but sensitivity for post-translational modification detection deteriorates
Solution Approach 1:
The invention performs preliminary enrichment and specific binding of post-translational modifications using highly specific binding agents before detection. This preliminary action concentrates the target PTMs and removes background interference, thereby maintaining high sensitivity for PTM detection while enabling high-throughput processing through subsequent automated sequencing of coding tags.
3Productivity
If multiple binding agents are used simultaneously for multiplexed analysis, then productivity is improved, but cross-reactivity between binding agents increases
Solution Approach 1:
The invention assigns unique local qualities to each binding agent through distinct coding tags (specific nucleic acid sequences). This local differentiation allows each binding agent to be specifically identified and tracked, enabling multiplexed analysis where multiple binding agents can be used simultaneously without cross-reactivity, as each binding event is uniquely coded and can be independently read out.
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
Enables highly-parallel, sensitive, and accurate characterization of proteins and peptides, overcoming limitations of existing methods by providing a high-throughput and multiplexed analysis capable of identifying and quantifying proteins and their modifications.
Implementation Method 1
Molecular recognition and characterization of a protein or peptide macromolecule is typically performed using an immunoassay
Implementation Method 2
enabling high-throughput and high-parallel collection of this proteomic information by miniaturizing and parallelizing protein analysis workflows and employing affinity reagents and nucleic acid encoding
Data Source
AI summary
A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.