Comparison of PRM and MRM: A Quantitative Proteomics Analysis

In proteomics research, targeted quantitative techniques play an increasingly important role from target discovery to result validation. Compared to traditional labeled quantification or Data-Dependent Acquisition (DDA) methods, Multiple Reaction Monitoring (MRM) and Parallel Reaction Monitoring (PRM) technologies offer higher specificity, sensitivity, and reproducibility, especially suitable for accurate detection of low abundance proteins. With the development of high-resolution mass spectrometry technology, PRM gradually shows potential to complement or even replace MRM in specific applications. This article systematically compares PRM and MRM in terms of technical principles, performance characteristics, applicable scenarios, and data processing, providing researchers with selection references.

 

1. Technical Principle Comparison

1、MRM（Multiple Reaction Monitoring）Using a Triple Quadrupole (QqQ) mass spectrometer, it achieves highly selective quantitative monitoring by setting the m/z of precursor ions and specific product ions.

2、PRM（Parallel Reaction Monitoring）Relies on high-resolution, high-precision mass spectrometry platforms (such as Orbitrap or Q-TOF) to perform a full product ion scan of target peptide segments, thereby obtaining more comprehensive ion information.

📌 In short, MRM is 'point-to-point' monitoring, while PRM is 'full-spectrum' capture.

 

2. Performance Comparison: Sensitivity vs. Specificity vs. Throughput

 

 

🎯 In terms of method development cycle, specificity, and data integrity, PRM has certain advantages, while MRM is still the first choice for ultra-high throughput and extreme sensitivity requirements.

 

3. Application Scenario Differences: From Large-Scale Screening to Precise Validation

✅ MRM is more suitable for:

• Quantification of known proteins in high-throughput clinical samples

• Quantitative analysis in the biomarker validation stage

• Research on the mechanism of drug action in the pharmaceutical industry

 

✅PRM is more suitable for:

• Verification of specific peptide segments in low abundance, complex background samples

• Target confirmation using DDA initial screening data

• Research requiring complete fragmentation spectra to enhance reliability

 

📌 For example, in cancer biomarker research, PRM is often used to validate candidate peptide segments identified by early DDA, followed by MRM for high-throughput detection in large-scale samples.

 

4. Data Processing and Software Support

Both technologies can utilize open-source software like Skyline for method development and data analysis, but there are differences in processing flow and complexity:

1、MRMFocus on specific ion pairs, clear data structure, fast processing speed, suitable for standardized applications;

2、PRMNeed to extract target signals from full product ion spectra, analysis involves spectrum reconstruction and interference peak elimination, requiring higher algorithm and personnel experience.

 

5. Cost and Instrument Accessibility Considerations

1、MRM Relies on triple quadrupole mass spectrometers, instruments are relatively common, low operating costs, is a routine platform for many hospitals and pharmaceutical companies.

2、PRM Requires high-resolution mass spectrometers like Orbitrap or Q-TOF, higher purchase and maintenance costs, suitable for research institutions or high-end quantitative needs.

 

6. How to Choose PRM or MRM?

PRM and MRM each have their merits, the key is to clarify research goals and sample characteristics:

• If pursuing maximum sensitivity and high throughput, MRM is preferred;

• If focusing on specificity and method development efficiency, PRM has more advantages;

• In practical applications, both can complement each other, forming a complete quantitative closed loop from discovery to validation.

 

📣 BGI Tech Bio combines years of mass spectrometry platform management experience and project service accumulation, has established high-throughput, standardized PRM/MRM quantitative analysis workflows, supporting various sample types (plasma, urine, FFPE, tissue, etc.), welcome to contact us for customized targeted proteomics solutions!

 

BGI Tech Bio--Characterization of biological products, high-quality service provider for multi-omics biological mass spectrometry detection

 

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