PRM-Based Analysis of Targeted Proteomics

Targeted proteomics is a critical approach for protein research, enabling the quantification of specific proteins or peptides. This technology plays a significant role in studying changes in protein expression and mechanisms within complex samples. Among various targeted proteomics methods, Parallel Reaction Monitoring (PRM) has gained attention due to its high sensitivity, specificity, and throughput.

 

PRM is a mass spectrometry (MS)-based targeted proteomics method, similar in principle to Multiple Reaction Monitoring (MRM) but with key differences in critical steps. In PRM analysis, target peptides are first separated through liquid chromatography (LC), then ionized and subjected to precursor ion selection using high-resolution mass spectrometers, such as Orbitrap or Q-TOF. The selected precursor ions are fragmented, generating multiple product ions that are simultaneously detected and quantified. This approach allows PRM to obtain rich information on product ions in a single analysis, enhancing the accuracy and specificity of quantification.

 

Advantages of PRM

1. High Sensitivity and Specificity

Due to the high-resolution and accurate mass measurement capabilities of the mass spectrometer, PRM can effectively distinguish isomers and background noise, making it possible to detect low-abundance proteins and peptides.

 

2. Simplified Experimental Workflow

Unlike traditional MRM methods, PRM does not require the selection of specific product ions for each target peptide, reducing method development time and complexity, thereby improving experimental efficiency.

 

3. High Throughput Analysis

PRM can monitor multiple target peptides simultaneously and conduct a comprehensive analysis of product ions, making it suitable for high-throughput research in complex systems.

 

Limitations of PRM

1. Instrument Dependency

PRM requires high-resolution, high-precision mass spectrometers like Orbitrap or Q-TOF, which increases experimental costs and necessitates high standards for instrument operation and maintenance.

 

2. Data Processing Complexity

PRM generates extensive product ion information in a single analysis, making data processing and analysis reliant on efficient software and stringent standardization procedures to ensure result reliability and consistency.

 

3. Applicability Restrictions

PRM is more suitable for studies with predefined targets, while its value is limited in exploratory research.

 

Applications of PRM in Biomedical Research

PRM has shown wide-ranging applications in various biomedical research fields, particularly in disease biomarker discovery, drug target validation, and signal pathway studies. For example, in cancer research, PRM can be used to quantify the expression changes of tumor-related proteins, helping researchers better understand tumor mechanisms and providing new targets for diagnosis and therapy. Moreover, in drug development, PRM is extensively used to study drug-target interactions, allowing precise evaluation of the effects of candidate drugs on target proteins.

 

As a critical tool in targeted proteomics research, PRM has become a commonly used method in protein quantification due to its high sensitivity, specificity, and throughput. Although challenges remain in data processing and instrument requirements, the continuous advancement of mass spectrometry technologies and data analysis methods suggests a promising future for PRM in the study of complex biological systems.