Polypeptide Identification via Binding Pool Fingerprinting
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Solution Overview
Problem
Current methods for identifying and quantifying proteins and polypeptides in samples are often slow, expensive, and inefficient, especially when dealing with low concentrations or complex mixtures, as they require direct sequencing which can be difficult and time-consuming.
Innovation Solution
A method involving the characterization of structural properties of polypeptides using binding pools with probes that recognize specific targets, followed by searching databases for matching sequences, allowing for the identification and quantification of polypeptides based on their binding profiles and digital signatures.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If direct sequencing is used to identify polypeptides, then accurate identification can be achieved, but the process becomes slow and expensive
Solution Approach 1:
The identification process is segmented into two stages: first, rapid fingerprinting provides initial identification information, and second, direct sequencing is performed only on ambiguous cases. This segmentation reduces the overall time and cost while maintaining accuracy by avoiding unnecessary sequencing of clearly identified polypeptides.
Solution Approach 2:
The fingerprinting method serves multiple functions: it provides rapid preliminary identification, filters out clearly identified polypeptides, and guides subsequent sequencing efforts. This multi-functional approach replaces the need for direct sequencing in all cases, significantly reducing time and cost while maintaining identification accuracy.
2Measurement precision
If direct sequencing is used to identify polypeptides, then accurate identification can be achieved, but the cost increases significantly
Solution Approach 1:
The identification process is segmented into two stages: first, rapid fingerprinting provides initial identification information, and second, direct sequencing is performed only on ambiguous cases. This segmentation reduces the overall time and cost while maintaining accuracy by avoiding unnecessary sequencing of clearly identified polypeptides.
Solution Approach 2:
The fingerprinting method serves multiple functions: it provides rapid preliminary identification, filters out clearly identified polypeptides, and guides subsequent sequencing efforts. This multi-functional approach replaces the need for direct sequencing in all cases, significantly reducing time and cost while maintaining identification accuracy.
3Measurement precision
If traditional methods are used to identify polypeptides in complex mixtures, then identification can be achieved, but the efficiency decreases
Solution Approach 1:
Fingerprinting is performed as a preliminary action before direct sequencing. This preliminary step rapidly characterizes polypeptides in complex mixtures, allowing researchers to identify clearly characterized polypeptides without sequencing and to focus sequencing efforts only on ambiguous cases, thereby significantly improving identification efficiency.
Solution Approach 2:
Instead of directly sequencing all polypeptides, the method creates a fingerprint copy or representation of each polypeptide's characteristics. These fingerprints serve as proxies that can be rapidly compared and analyzed, replacing the need for time-consuming direct sequencing in many cases while maintaining identification accuracy.
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 approach enables efficient identification and quantification of polypeptides by determining the presence of binding pool targets and matching them to database sequences, providing both relative and absolute quantification, even in complex samples, with improved speed and accuracy compared to traditional sequencing methods.
Implementation Method 1
each binding pool comprises one or more probes, each probe of which can recognize and bind a binding pool target
Data Source
AI summary
Methods are disclosed for identifying one or more proteins or polypeptides comprised by a sample. The methods comprise determining binding of each polypeptide with respect to each binding pool of a plurality of binding pools, wherein each binding pool comprises one or more probes which bind a structure comprised by a protein or polypeptide. In some aspects, polypeptides can be denatured and separated into individual polypeptide strands and immobilized on a solid support prior to determining binding of the binding pools. A protein, polypeptide or polypeptide strand can be identified by searching, in at least one database, for a protein or polypeptide sequence comprising binding pool targets either identical to or most similar to the binding pool targets comprised by the protein, polypeptide or polypeptide strand to be identified. Kits for identifying proteins, polypeptides and polypeptide strands are also disclosed.