Automated Peptide Preparation for High-Throughput Mass Spectrometry
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Solution Overview
Problem
Current mass spectrometric methods for proteomics face challenges such as low sample preparation throughput, low protein identification rates, and lengthy instrument time, particularly in large-scale plasma proteome profiling, leading to incomplete separation and impaired identification of peptides.
Innovation Solution
A method involving combining peptides or polypeptides into a plex, splitting and recombining portions for analysis, and using chemically isotopic labeling to enhance quantification and identification through mass spectrometry, with automated liquid handling and specific clean-up techniques.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If mass spectrometric methods are used for proteomics analysis, then sensitivity and quantitative capability are improved, but sample preparation throughput remains low and instrument time is lengthy
Solution Approach 1:
The patent applies segmentation by dividing the complex proteomics analysis into distinct modules: automated sample preparation, isotopic labeling, mass spectrometry analysis, and data processing. The automated liquid handling system separates sample preparation tasks from instrument analysis, allowing parallel processing of multiple samples and increasing throughput while maintaining sensitivity through standardized protocols
Solution Approach 2:
The patent implements preliminary action through automated sample preparation and isotopic labeling performed before mass spectrometry analysis. The automated liquid handling system prepares samples in advance with precise reagent addition and mixing, and isotopic labels are incorporated during sample preparation rather than during analysis, enabling higher throughput without compromising measurement precision
2Measurement precision
If mass spectrometric methods are used for proteomics analysis, then sensitivity and quantitative capability are improved, but instrument time becomes lengthy
Solution Approach 1:
The patent performs isotopic labeling and sample preparation in advance before instrument analysis, so that when samples reach the mass spectrometer, they are ready for rapid analysis. The automated liquid handling system completes all preparatory steps including reagent addition, mixing, and incubation before sample injection, reducing instrument time while maintaining sensitivity through pre-optimized labeling protocols
Solution Approach 2:
The patent implements streamlined workflows that skip unnecessary steps in the mass spectrometry process. The automated system uses pre-programmed sequences for rapid sample injection and analysis, and the isotopic labeling approach allows for faster data acquisition by eliminating the need for complex post-processing steps, thereby reducing instrument time while preserving sensitivity
3Ease of manufacture
If proteolysis of complex biological samples is performed, then protein digestion is achieved, but thousands of peptides are produced that overwhelm chromatographic and mass spectrometric systems causing incomplete separation and impaired identification
Solution Approach 1:
The patent applies segmentation by dividing the complex mixture of thousands of peptides into smaller, more manageable groups through automated liquid handling and chromatographic separation. The system processes peptides in fractions or batches, separating them by physical or chemical properties, which reduces the complexity presented to the mass spectrometer at any given time and improves identification accuracy while maintaining complete digestion
Solution Approach 2:
The patent introduces intermediary steps between proteolysis and mass spectrometry analysis, including automated liquid handling for sample preparation and chromatographic separation. These intermediary processes act as mediators that organize and pre-process the complex peptide mixture, reducing overwhelming complexity before samples enter the mass spectrometer and improving peptide identification
4Quantity of substance
If large-scale plasma proteome profiling is performed, then comprehensive proteome coverage is achieved, but throughput is limited due to lengthy preparation and instrument time
Solution Approach 1:
The patent segments large-scale plasma proteome profiling into multiple parallel processing streams using automated liquid handling. Multiple samples are prepared simultaneously in separate channels, and the system can process multiple plexes in parallel, maintaining comprehensive proteome coverage across all samples while increasing overall throughput through concurrent processing
Solution Approach 2:
The automated liquid handling system performs multiple functions within a single platform: sample preparation, isotopic labeling, mixing, and preparation for mass spectrometry analysis. This multi-functional approach allows the same system to handle diverse sample types and processing requirements, achieving comprehensive proteome coverage across different sample conditions while maintaining high throughput through operational efficiency
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 improves the efficiency and accuracy of peptide and protein identification, reducing processing time and cost while maintaining high reproducibility, enabling large-scale proteome profiling with enhanced throughput and reduced instrument time.
Implementation Method 1
quantifying or identifying two or more chemically isotopic labeled peptides or polypeptides
Implementation Method 2
analyzing the peptides or polypeptides so as to obtain mass spectrometry data
Data Source
AI summary
Provided herein are methods of quantifying or identifying two or more peptides or polypeptides, methods of quantifying or identifying two or more chemically isotopic labeled peptides or polypeptides, and methods for obtaining a plurality of enriched peptides or polypeptides in a sample.