Overview of Targeted Proteomics: Methods, Techniques, Key Points, and Applications
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Integrated Instrumentation Platforms: Our services are powered by Agilent 6495 and SCIEX QTRAP triple quadrupole systems, as well as high-resolution PRM analysis via the Orbitrap Exploris platform. We also support SWATH-MS acquisition and spectral library generation.
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Customized Method Development: We provide flexible assay development, including target selection and the synthesis of stable isotope-labeled (SIS) peptides to accommodate project-specific needs.
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Standardized Workflow Management: Our end-to-end quality control system spans sample preparation, instrument operation, and data analysis to ensure consistency and reliability.
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Hybrid DIA and Targeted Strategies: Our integrated approach bridges the discovery and validation phases, supporting the development of robust biomarker pipelines.
With the increasing emphasis on precision, quantification, and clinical translation in life science research, Targeted Proteomics has emerged as a pivotal tool for advancing proteomic discoveries into clinical applications. Characterized by high sensitivity, high reproducibility, and high specificity, this approach serves as a vital link between omics-based findings and practical implementation. It is particularly well-suited for applications such as biomarker validation, pharmacodynamic studies, immune monitoring, and quality control.
What Is Targeted Proteomics?
Targeted Proteomics relies on mass spectrometry as its primary analytical platform. A defining feature of this approach is the preselection of specific target peptides, followed by their targeted acquisition and quantitative analysis. The three principal strategies currently in use are:
1. MRM/SRM (Multiple/Selected Reaction Monitoring)
Based on triple quadrupole mass spectrometry, this method monitors predefined transitions (precursor-to-product ion pairs) and is widely employed for high-throughput validation across large sample cohorts.
2. PRM (Parallel Reaction Monitoring)
Utilizing high-resolution mass spectrometers such as the Orbitrap, PRM allows comprehensive detection of all fragment ions derived from a selected precursor, thereby enhancing both specificity and the reusability of the acquired data.
3. SWATH-MS (Sequential Window Acquisition of All Theoretical Fragment Ions)
A form of data-independent acquisition (DIA), SWATH-MS captures fragment ion data across sequential mass windows, enabling retrospective, quasi-targeted quantitative analysis through post-acquisition data mining.
It is important to note that while SWATH-MS is capable of targeted-like analysis, it fundamentally belongs to the category of DIA techniques. In practice, it is often employed for the initial screening of candidate targets and for quantitative studies at intermediate throughput scales.
Key Technical Points of Targeted Proteomics
1. Peptide Selection Strategy
(1) Unique to the target protein
(2) High ionization efficiency
(3) Chemically stable, free of modifications or labile residues
2. Internal Standard Introduction and Quantification Methods
(1) Relative quantification: based on the comparison of peptide peak areas
(2) Absolute quantification: achieved by introducing stable isotope-labeled peptides (SIS) to correct for systematic errors
3. Standardized Experimental Workflow
(1) Sample processing, including extraction, enzymatic digestion, and purification
(2) Instrument parameter optimization, such as collision energy and retention time window
(3) Data analysis using dedicated software tools, including Skyline and Spectronaut
Advantages and Limitations of Targeted Proteomics
1. Advantages
2. Limitations
(1) Dependence on prior knowledge limits its use in the identification of novel proteins
(2) Method development requires further optimization, particularly in transition selection for MRM assays
Typical Applications of Targeted Proteomics
1. Validation of Disease Biomarkers
(1) Early cancer screening, e.g., PRM-based validation of candidate protein biomarkers in breast cancer
(2) Assessment of protein biomarkers associated with autoimmune diseases
(3) Stratification of high-risk individuals in cardiovascular disorders based on protein expression profiles
2. Evaluation of Drug Targets and Therapeutic Efficacy
(1) Monitoring the regulation of key signaling proteins in response to pharmacological treatment
(2) Longitudinal PRM-based tracking of dynamic proteomic changes throughout the treatment course
3. Liquid Biopsy and Complex Sample Profiling
(1) Targeted proteomics is well-suited for the analysis of complex biological fluids such as plasma, urine, and cerebrospinal fluid
(2) Enables the detection of tumor-derived proteins present at very low abundance levels
4. Monitoring in Synthetic Biology and Microbial Cell Factories
(1) Precise quantification of critical enzymes involved in engineered metabolic pathways
(2) Facilitates the regulation and optimization of recombinant protein expression in microbial systems
Distinct Features of Targeted Proteomics Services at MtoZ Biolabs
MtoZ Biolabs offers a comprehensive targeted proteomics platform incorporating MRM, PRM, and DIA/SWATH strategies, tailored to support both basic research and translational studies:
As a powerful tool for protein quantification, targeted proteomics is increasingly recognized as a key interface between basic research and clinical translation. By selecting the appropriate method—MRM, PRM, or SWATH—researchers can achieve highly sensitive, reproducible quantification of critical proteins. MtoZ Biolabs is dedicated to delivering accurate and reliable targeted proteomics services to accelerate the understanding of disease mechanisms, biomarker validation, and biotherapeutic development.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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