Peptide Barcode Sequencing for Multiplex Protein Identification
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Solution Overview
Problem
Next-generation DNA sequencing technologies have struggled to capture the complex and dynamic states of proteins due to scale and amplification challenges, limiting the understanding of proteomics.
Innovation Solution
The use of peptide-based proximity ligation methods, where affinity reagents attached to peptide tags bind to target analytes, allowing for the formation of complexes that are sequenced to identify proteins, overcoming limitations of traditional oligonucleotide-based methods.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If oligonucleotide-based sequencing methods are used for protein identification, then amplification capability is improved, but manufacturing complexity and inability to capture dynamic protein states worsen
Solution Approach 1:
The patent introduces peptide tags as intermediary molecules that bridge proteins and sequencing detection. These peptide tags are attached to proteins of interest and contain encodable sequences that can be detected by sequencing technologies, enabling protein identification without requiring protein amplification while maintaining compatibility with existing sequencing infrastructure
Solution Approach 2:
The patent replaces the need for biochemical amplification mechanisms (PCR for DNA) with a direct tagging and detection approach. By attaching peptide tags with encodable sequences directly to proteins, the system eliminates the amplification step while maintaining detectability through sequencing methods
2Quantity of substance
If traditional proteomics methods are used, then protein scale coverage is limited, but measurement precision and dynamic state capture worsen
Solution Approach 1:
The patent segments the protein identification process into two independent components: the protein of interest and the attached peptide tag with encodable sequence. This segmentation allows the tag to carry identification information that can be precisely read by sequencing methods, enabling accurate detection of protein presence and state without being limited by traditional proteomics coverage
Solution Approach 2:
The patent changes the detection parameter from direct protein analysis to sequencing-based detection of attached peptide tags. This parameter change enables the use of highly precise sequencing technologies to identify proteins and their states, significantly improving measurement precision and the ability to capture dynamic protein states
3Adaptability or versatility
If peptide tags with encodable sequences are used instead of oligonucleotides, then adaptability to protein modifications is improved, but manufacturing precision requirements worsen
Solution Approach 1:
The patent designs peptide tags with encodable sequences that serve multiple functions: they can be attached to various proteins, accommodate different protein modifications, and maintain compatibility with sequencing detection. This universal design allows the same tag structure to be used across diverse protein targets and modification types
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 the identification of multiple proteins within a sample with improved accuracy and efficiency, facilitating medical diagnosis and biotechnology research by leveraging the broader modifications and in situ sequencing capabilities of peptides.
Implementation Method 1
the first affinity reagent and the second affinity reagent are each configured to bind a target analyte to form a complex comprising the first affinity reagent, the second affinity reagent, and the target analyte
Data Source
AI summary
The present disclosure relates to methods and compositions for protein identification via peptide barcodes.