Targeted Proteomics Service

MtoZ Biolabs provides professional Targeted Proteomics Services using Parallel Reaction Monitoring (PRM), Multiple/Selected Reaction Monitoring (MRM/SRM), and stable isotope-assisted absolute quantification strategies such as AQUA. Our workflows enable sensitive, specific, and reproducible quantification of predefined proteins or peptides for biomarker validation, discovery proteomics verification, low-abundance protein analysis, PTM studies, and relative or absolute quantification.

When This Service Is a Good Fit

Targeted proteomics is best suited for studies with predefined proteins or peptides where the goal is validation, comparison, or precise quantification rather than broad protein discovery.

Research Need	How Targeted Proteomics Helps
Validate candidates identified by DIA, TMT, or label-free proteomics	PRM or MRM/SRM provides targeted quantitative verification
Verify disease-, drug response-, or pathway-related proteins	Enables selective and reproducible quantification across multiple samples
Measure low-abundance proteins or targets lacking reliable antibodies	Uses sequence-specific peptides and reduces dependence on antibodies
Analyze PTM peptides or distinguish highly homologous proteins	Uses specific peptides and fragment-ion information for confident detection
Compare protein changes or determine actual abundance	Supports relative and isotope-assisted absolute quantification

No target list yet? If your study is still in the discovery stage, Discovery Proteomics may be a better starting point before targeted validation.

Targeted Proteomics Service at MtoZ Biolabs

MtoZ Biolabs designs customized targeted proteomics workflows based on target number, sample type, protein abundance, quantification requirements, and project scale. Our services include:

• Targeted quantification of predefined proteins and peptides
• Selection of PRM or MRM/SRM strategies according to project needs
• Relative and absolute quantification
• Stable isotope-labeled peptide-assisted absolute quantification
• Validation of candidate proteins identified by DIA, label-free, TMT, iTRAQ, and other discovery proteomics workflows
• Detection of low-abundance target proteins in complex biological samples
• Targeted quantification of specific PTM peptides, including phosphorylation, acetylation, and ubiquitination
• Antibody-independent protein detection for targets lacking high-quality antibodies

Choose the Right Targeted Proteomics Workflow

Choosing a workflow requires defining both the quantification goal and the MS acquisition strategy.

Comparison	Relative Quantification	Absolute Quantification
Core question	How much does the target change between samples?	How much target is actually present?
Typical output	Fold change, relative abundance, normalized intensity	fmol, pmol, ng/mL, μg/mL
Internal standard	Usually not required for absolute calibration	Stable isotope-labeled standards are typically required
Common workflow	PRM or MRM/SRM	PRM or MRM/SRM + isotope-labeled standards
Main advantage	Flexible and efficient for group comparisons	Provides actual amount or concentration
Best suited for	Candidate validation, group comparison, treatment and time-course studies	Biomarker quantification, precise measurement, standardized assays

After defining the quantification goal, PRM or MRM/SRM can be selected according to target number, sample scale, complexity, and assay maturity.

Comparison	PRM	MRM/SRM
Typical platform	High-resolution mass spectrometer	Triple quadrupole mass spectrometer
Acquisition	Collects high-resolution fragment-ion spectra from selected precursors	Monitors predefined precursor-to-product ion transitions
Main advantage	Rich fragment information, high specificity, flexible development	High reproducibility and robust quantitative performance
Target scale	Small to medium target sets	Fixed panels and larger routine target sets
Best suited for	Candidate validation, discovery result verification, complex samples, PTM peptides	Biomarker panels, multi-sample studies, large cohorts, routine monitoring
Method development	Less transition optimization upfront	Usually requires more extensive transition optimization

Service Advantages

1. Multiple Quantification Strategies

PRM, MRM/SRM, and isotope-assisted absolute quantification are available for different study goals.

2. Antibody-Independent Detection

Sequence-specific peptide measurement reduces reliance on commercial antibodies.

3. High Selectivity in Complex Samples

Target-focused acquisition improves selective detection of predefined peptides.

4. Discovery-to-Validation Support

DIA, label-free, TMT, and iTRAQ discovery results can be followed by PRM or MRM/SRM validation.

5. Customized Method Development

Methods can be optimized for target peptides, acquisition parameters, matrix interference, sensitivity, and quantitative stability.

Analysis Workflow

1. Project Evaluation

Define targets, sample type, sample number, and quantification goals.

2. Peptide Selection

Select suitable target peptides based on specificity and MS detectability.

3. Method Development

Choose PRM or MRM/SRM and optimize acquisition parameters.

4. Sample Preparation

Perform protein extraction, digestion, peptide cleanup, and enrichment when needed.

5. LC-MS/MS Analysis

Selectively acquire predefined protein or peptide targets.

6. Data Analysis & Reporting

Perform signal extraction, QC, quantification, and final reporting.

Sample Submission Requirements

Item	Requirement
Total protein	20–50 μg minimum; ≥50 μg recommended
Protein concentration	>0.5 μg/μL recommended
Sample purity	SDS and other detergent residues should be <0.1%
Nucleic acid contamination	No obvious viscosity or stringiness caused by nucleic acids
Sample condition	Homogeneous, without obvious precipitation or degradation; avoid repeated freeze-thaw cycles

Applications of Targeted Proteomics

1. Candidate Protein Validation

Verify differential proteins identified by DIA, TMT, label-free, or iTRAQ workflows.

2. Biomarker Research

Quantify disease-, prognosis-, or drug response-related candidate proteins across study cohorts.

3. Drug Development and Mechanism Studies

Monitor target proteins, pathway proteins, and pharmacodynamic markers before and after treatment.

4. Pathway and Functional Protein Analysis

Quantify predefined proteins within signaling, metabolic, or functional pathways.

5. PTM and Precision Quantification

Analyze phosphorylation, acetylation, ubiquitination, and other modified peptides, with absolute quantification available when isotope-labeled standards are used.

Deliverables

1. Target Protein and Peptide Information

2. PRM/MRM Results

3. Quantitative Results

4. Quality Control Results

5. Statistical and Visualization Results

6. Raw Data and Final Report

Frequently Asked Questions

Q1. What is the difference between targeted and untargeted proteomics?

Untargeted proteomics broadly identifies and quantifies proteins without predefined targets, while targeted proteomics selectively measures known proteins or peptides. Discovery Proteomics focuses on finding candidates, whereas Targeted Proteomics focuses on verification and precise quantification.

Q2. Can targeted proteomics detect low-abundance proteins?

Yes. Targeted acquisition can improve selectivity for low-abundance proteins, although performance still depends on target abundance, peptide properties, matrix interference, and instrument sensitivity. Enrichment or optimized sample preparation may be required for very low-abundance targets.

Q3. What information should I provide for a quotation?

Please provide the target protein list, species, sample type, sample number and groups, relative or absolute quantification requirements, PTM information if applicable, and any existing DIA, TMT, or other discovery proteomics data.

Q4. How long does a targeted proteomics project take?

A typical project takes approximately 3–4 weeks. Expedited projects may be completed in about 3 weeks, depending on instrument availability. Sample QC failures, large-cohort batch processing, and customized data analysis may extend the timeline.

Start Your Targeted Proteomics Project

If you already have a target protein list, candidate biomarkers, or differential proteins identified by DIA, TMT, label-free, or iTRAQ proteomics, send us your project information for a feasibility assessment.

Our technical team can evaluate your targets, samples, and study goals and recommend an appropriate workflow, sample submission plan, and quotation.

Submit your project information to start your targeted proteomics study.