What Is the Difference between Targeted and Untargeted Proteomics

Targeted proteomics and untargeted proteomics represent two widely used but fundamentally different strategies in proteomics research. They differ significantly in research objectives, methodological approaches, data output, and appropriate application scenarios. A clear understanding of their distinctions is crucial for researchers to design experiments effectively, interpret results accurately, and select suitable analytical platforms.

 

Different Research Objectives: Quantitative Accuracy vs. Comprehensive Exploration

1. Untargeted Proteomics: Broad Profiling with an Exploratory Focus

Untargeted proteomics, also referred to as discovery proteomics, aims to identify and quantify as many proteins as possible in a sample without predefining specific targets. It typically employs data-dependent acquisition (DDA) or data-independent acquisition (DIA) strategies.

This approach is particularly well-suited for:

• Biomarker discovery

• Investigating disease mechanisms

• Initial exploration of complex biological systems

 

2. Targeted Proteomics: Precise Quantification for Hypothesis-Driven Validation

Targeted proteomics focuses on the quantitative analysis of selected proteins or peptides that have been identified in prior studies. It offers high sensitivity and reproducibility, commonly using multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) for data acquisition.

This approach is commonly applied to:

• Biomarker validation

• Development of clinical diagnostic assays

• Targeted monitoring in pharmacodynamic and toxicological studies

 

Differences in Experimental Design: Openness vs. High Customization

 



 

Data Output Format: Quantity vs Accuracy

• Untargeted proteomics: outputs identification and quantification information for thousands of proteins, allowing construction of protein expression profiles, pathway enrichment, clustering analysis, etc.

• Targeted proteomics: outputs precise abundance data for dozens to hundreds of specific proteins, more suitable for building quantitative models, comparisons under controlled conditions, etc.

 

For example, in cancer biomarker development, untargeted is used to discover candidate proteins, while targeted is used to further validate the expression differences of these candidate biomarkers in large sample cohorts.

 

Applications

 



 

Currently, an increasing number of studies employ a combined approach of untargeted discovery followed by targeted validation. This strategy leverages the strengths of both methods to enhance the depth and reliability of research findings.

 

Targeted and untargeted proteomics should not be regarded as mutually exclusive or hierarchically superior. Rather, they represent essential and complementary stages within the continuum of exploration, validation, and application. Scientific investigations typically begin with broad, untargeted proteomic screening and progress toward precise, targeted validation. The integration of both approaches is fundamental to building a robust and dependable proteomics research framework. MtoZ Biolabs utilizes high-throughput mass spectrometry platforms to provide targeted proteomics analysis services, including MRM- and PRM-based quantitative proteomics as well as absolute quantification. Please feel free to contact us for customized technical consultation and service solutions.

 

MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.

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Targeted Proteomics Service