Nanowell Array Layout for Low-Loss Single-Cell Proteomics
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Solution Overview
Problem
Current mass spectrometry-based proteomic analysis requires large sample volumes, limiting the analysis of small samples and the ability to resolve microheterogeneity within tissues, and there is a need for devices and methods to reduce sample processing volumes and enhance biochemical sample measurements for high-throughput single-cell proteomic technologies.
Innovation Solution
A device comprising a substrate with arrays of reaction vessels, each with a hydrophilic surface and surrounded by a hydrophilic ring, allowing for nanoliter-scale sample processing and pooling of reaction vessel contents for improved biochemical quantification, minimizing losses and enabling efficient sample handling operations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of substance
If conventional sample processing methods are used, then sufficient sample volume is available for analysis, but significant protein and peptide loss occurs due to nonspecific adsorption and evaporation
Solution Approach 1:
The invention changes the physical parameters of the reaction vessels by reducing their volume to nanoliter scale (1-100 nL), which fundamentally alters the surface-to-volume ratio and minimizes nonspecific adsorption. This parameter change resolves the contradiction by maintaining sufficient sample quantity while reducing substance loss through evaporation and adsorption.
Solution Approach 2:
The invention segments the sample processing into multiple independent nanowell reactions, each containing minimal sample volume. By dividing the total sample into many small compartments, the system maintains adequate overall sample quantity while each segment experiences reduced loss, resolving the contradiction between sample volume and substance loss.
2Measurement precision
If large sample volumes are used for proteomic analysis, then sufficient material is available for detection, but the ability to resolve microheterogeneity within tissues is limited
Solution Approach 1:
The invention segments tissue samples into individual cells or small cell populations, with each cell processed in a separate nanowell. This segmentation enables resolution of microheterogeneity by maintaining spatial separation of individual cells while using nanoliter volumes that preserve sufficient protein material for detection, thus resolving the contradiction between measurement precision and quantity of substance.
Solution Approach 2:
The invention applies local quality by creating unique microenvironments in each nanowell that preserve the specific biochemical characteristics of individual cells or small populations. This local preservation of sample integrity enables precise measurement of microheterogeneity while maintaining sufficient protein quantity for analysis.
3Productivity
If conventional reaction vessels are used, then standard processing protocols can be applied, but digestion kinetics are inefficient and sample throughput is limited
Solution Approach 1:
The invention changes the physical parameters of the reaction environment by using nanoliter-scale vessels, which fundamentally alters mass transport and reaction kinetics. The reduced volume enhances diffusion rates and enzyme-substrate interactions, improving digestion kinetics while enabling parallel processing of many samples, thus resolving the contradiction between productivity and duration of action.
Solution Approach 2:
The invention transitions from conventional microliter-scale processing to nanoliter-scale processing, representing a dimensional change in the reaction volume regime. This dimensional shift enables both improved kinetics through enhanced mass transport and increased throughput through parallelization, resolving the contradiction between productivity and reaction time.
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
The device enables deep, quantitative proteome profiling of small samples by reducing processing volumes and sample losses, facilitating analysis of nanoscale biological samples with improved peptide quantification and high-throughput capabilities.
Implementation Method 1
Each reaction vessel has a hydrophilic surface... A hydrophilic ring surrounds each array... unoccupied regions of the upper surface of the substrate are hydrophobic
Implementation Method 2
Each reaction vessel has a hydrophilic surface and a diameter of from greater than 0 mm to 0.8 mm
Data Source
AI summary
A device for biological sample preparation and analysis is disclosed. The device includes a substrate and a plurality of spaced apart arrays disposed on an upper surface of the substrate. Each array includes a plurality of reaction vessels, each reaction vessel having a hydrophilic surface. A hydrophilic ring surrounds each array. Methods of making and using the device are also disclosed.