What is Targeted Quantitative Proteomics
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High throughput with minimal background interference
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Suitable for the quantification of dozens to hundreds of targets
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Based on principles consistent with MRM applications in metabolomics
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Offers higher analytical accuracy and improved specificity
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Well-suited for identifying targets within complex biological matrices
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Applicable during validation phases or for the analysis of clinical samples
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Enhanced peptide coverage
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Suitable for high-throughput quantification across diverse sample sets
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Candidate targets are identified based on prior data-independent acquisition (DIA) analyses, published literature, and curated databases (e.g., PeptideAtlas).
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Peptides selected for quantification are required to be stable, highly specific, and possess efficient ionization properties.
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Customized target design based on literature mining, DIA data integration, and target prioritization
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High-quality synthesis of stable isotope-labeled peptides tailored to client specifications
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Standardized data analysis workflows ensuring reproducibility and cross-sample comparability
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End-to-end solutions spanning discovery-phase proteomics to targeted validation
Targeted Quantitative Proteomics is an analytical approach in proteomics characterized by high sensitivity and specificity. It is widely applied in biomarker validation, elucidation of disease mechanisms, pharmacodynamic assessment, and quality control. Compared with discovery-based proteomics, targeted quantification emphasizes precise and highly reproducible quantitative analysis of predefined target proteins.
This article systematically outlines the fundamental principles, mainstream technical platforms, experimental workflows, and representative applications of targeted quantitative proteomics, aiming to assist researchers in making informed choices about appropriate technological strategies.
What Is Targeted Quantitative Proteomics?
Targeted quantitative proteomics focuses on preselected proteins or peptides, acquiring quantitative information by configuring specific ion transitions or employing full product ion scanning strategies. Key features of this approach include:
1. Clearly defined targets (specific proteins or peptide sequences)
2. Quantification calibrated using reference standards or internal standards
3. High reproducibility, suitable for clinical and large-cohort studies
4. Significantly higher sensitivity than discovery-based proteomics
Mainstream Technical Platforms
MRM/SRM (Multiple/Selected Reaction Monitoring)
(1) Instrumentation: Triple Quadrupole Mass Spectrometer
(2) Principle: Specific precursor ions are selected, subjected to fragmentation, and the resulting product ions are selectively detected
(3) Features:
2. PRM (Parallel Reaction Monitoring)
(1) Instrument platform: High-resolution mass spectrometers (e.g., Orbitrap, Q-TOF)
(2) Principle: Selection of precursor ions followed by simultaneous acquisition of all associated product ions
(3) Characteristics:
3. DIA-based Targeted Method
(1) Development trend: Integration of high-resolution data-independent acquisition (DIA) techniques, guided by internal standards to enable efficient targeted analysis
(2) Advantages:
Comparison Between Targeted Quantitative Proteomics and Discovery Proteomics
Overview of Targeted Quantitative Proteomics Experimental Workflow
1. Target Selection and Peptide Design
2. Synthesis of Standards (Optional)
Stable isotope-labeled peptides (SIS) are synthesized for the purpose of absolute quantification.
3. Sample Pretreatment
Samples undergo protein extraction, enzymatic digestion, and purification, followed by the addition of internal standards.
4. Mass Spectrometry Analysis
Depending on the research objective, either multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) is employed.
5. Data Processing and Quantitative Analysis
Quantitative data are analyzed using specialized software platforms, such as Skyline, SkyQuant, or Scaffold DIA.
Application Scenarios of Targeted Quantitative Proteomics
1. Biomarker Validation
In studies involving cancer, autoimmune disorders, or infectious diseases, targeted proteomics techniques such as MRM or PRM are frequently applied to validate candidate proteins identified in discovery-phase analyses, thereby facilitating translational research.
2. Pharmacodynamic and Toxicological Evaluation
By quantifying expression changes in specific proteins before and after pharmacological intervention, researchers can assess the modulation of drug targets and signaling pathways, supporting efficacy and safety evaluations.
3. Synthetic Biology and Optimization of Protein Expression
During the development of engineered cell systems, targeted quantification of key enzymes enables the evaluation and optimization of expression efficiency, improving the performance of microbial or cellular production platforms.
4. Quality Control and Batch-to-Batch Consistency Assessment
In biopharmaceutical manufacturing (e.g., antibodies, recombinant proteins), targeted proteomics is employed to monitor specific protein impurities and the expression of critical functional sites, supporting consistent product quality across batches.
MtoZ Biolabs offers a comprehensive suite of targeted quantitative proteomics services by integrating highly sensitive triple quadrupole mass spectrometry with high-resolution Orbitrap platforms. The available service formats include MRM-based quantification, PRM-based quantification, and stable isotope-labeled internal standard approaches. These services include:
Targeted quantitative proteomics represents a critical transition from broad-scale screening to precise molecular targeting. Its growing importance in disease mechanism research, clinical translation, and biopharmaceutical development underscores its value. Through the strategic selection of appropriate platforms (MRM or PRM) and careful experimental design, researchers can achieve highly sensitive, stable, and reproducible quantification of target proteins.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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