DIA+PRM Target Proteomics Services

MtoZ Biolabs provides DIA+PRM Target Proteomics Services by combining DIA quantitative proteomics with parallel reaction monitoring (PRM) targeted quantification. The service supports studies that require broad proteome screening followed by focused quantitative analysis of selected candidate proteins or peptides.

DIA provides broad quantitative proteome information for candidate discovery, while PRM focuses on predefined targets for follow-up quantification. Together, they support a continuous workflow from discovery and candidate prioritization to targeted analysis.

Technical Principles

DIA divides a predefined precursor mass range into consecutive isolation windows and systematically acquires MS/MS data from the ions within each window. Computational analysis is then used for peptide and protein identification and relative quantification.

PRM is a targeted mass spectrometry approach. Selected peptide precursor ions are isolated and analyzed by high-resolution MS/MS, allowing multiple fragment ions to be evaluated for peak characteristics, signal consistency, and interference.

Li J. et al. Drug Discovery Today Technologies. 2021.

Figure 1. The Principle of DIA and PRM

In a DIA+PRM workflow, DIA is first used for broad quantitative profiling and candidate screening. Representative peptides from selected proteins are then analyzed by PRM for focused quantitative evaluation.

When This Service Is a Good Fit

1. Prioritizing Candidates After DIA Discovery

DIA identifies multiple differential proteins, but the study needs to focus on a smaller set of biologically relevant candidates.

2. Evaluating Candidates in Independent Samples

Proteins identified during discovery need targeted quantitative comparison in an additional sample set.

3. Focusing on Pathway Proteins After Intervention

Drug treatment, genetic manipulation, or other interventions produce broad proteomic changes that require focused analysis of key pathway proteins.

4. Tracking Defined PTM Peptides

Specific modification sites or modified candidate peptides have already been identified and require targeted PRM evaluation.

DIA+PRM Target Proteomics Service at MtoZ Biolabs

MtoZ Biolabs provides an integrated workflow that can include sample evaluation, protein extraction and digestion, DIA LC-MS/MS analysis, protein identification and quantification, candidate screening, PRM target design, PRM LC-MS/MS analysis, and targeted quantitative data evaluation.

For studies without predefined candidates, DIA can be used first to identify proteins of interest. If a candidate protein list is already available from previous proteomics studies, the project can proceed directly to PRM feasibility evaluation and targeted analysis.

Analysis Workflow

1. Sample Preparation

Protein extraction, quantification, reduction and alkylation, digestion, peptide cleanup, and necessary quality control are performed according to sample type.

2. Chromatographic Separation and DIA Acquisition

Peptides are separated by liquid chromatography, followed by DIA acquisition for protein identification and relative quantification.

3. DIA Data Analysis and Candidate Screening

Proteins are identified and quantified, followed by between-group comparison and candidate selection based on quantitative changes, biological relevance, and peptide detectability.

4. PRM Target Design and Analysis

Representative peptides are selected for candidate proteins, followed by PRM method design and high-resolution targeted MS/MS acquisition.

5. Data Evaluation and Integration

PRM chromatographic and fragment-ion results are evaluated together with DIA data to assess candidate protein changes.

If reliable DIA results or a defined candidate list are already available, the project can proceed directly to PRM target evaluation.

Service Advantages

1. High-Resolution DIA Mass Spectrometry Platforms

MtoZ Biolabs uses high-resolution platforms including Orbitrap Exploris 480 and Astral for DIA data acquisition and quantitative proteomics analysis of complex samples.

2. Ion Mobility-Enhanced Separation

The timsTOF platform provides ion mobility separation capabilities that can support improved separation of complex peptide mixtures and high-throughput DIA analysis.

3. Flexible Support for Complex Samples

The service supports tissues, cultured cells, microorganisms, biofluids, and other common biological samples. The workflow can be adjusted according to sample number, complexity, and research objective.

Sample Submission Suggestions

Item	Recommendation
Applicable Samples	Animal and plant tissues, cultured cells, microorganisms, biofluids, and other samples with an available reference protein database
Total Protein	>20 μg/sample; ≥50 μg/sample recommended
Protein Concentration	>0.5 μg/μL
Sample Quality	Avoid severe degradation and minimize salts, detergents, and other LC-MS/MS-interfering components
Shipping	Low-temperature storage and dry-ice shipping are recommended
Species Information	Provide the species and confirm availability of a suitable reference database
PRM Target Information	Provide protein names, accession IDs, or peptide sequences if targets are already available

Actual sample requirements may vary with sample type and project design. Limited-input samples, complex biofluids, and combined DIA+PRM projects should be evaluated before submission.

Applications

1. Candidate Biomarker Research

DIA can screen differential proteins across experimental groups, followed by PRM quantification of selected candidates for subsequent research evaluation.

 

2. Drug Action and Target-Related Research

Proteome-wide responses to drug treatment can be profiled by DIA, followed by PRM analysis of selected proteins, pathways, or candidate targets.

 

3. Pathway-Focused Protein Analysis

When DIA indicates changes in a biological pathway or protein network, representative proteins can be selected for targeted PRM analysis.

 

4. Genetic or Phenotypic Intervention Studies

DIA can characterize broad protein changes associated with gene knockout, overexpression, or phenotype differences, followed by PRM quantification of selected candidates.

 

Deliverables

3. DIA Relative Quantitative Data

4. Differential Protein Analysis

5. Candidate Protein and Peptide Information

6. PRM Target Peptide Results

7. PRM Chromatographic and Fragment-Ion Data

8. Target Protein Quantitative Results

Final deliverables depend on whether the project includes DIA, PRM, or the complete DIA+PRM workflow.

 

FAQ

1. What Is the Difference Between DIA and PRM?

DIA is used for broad quantitative proteome profiling, whereas PRM focuses on predefined proteins or peptides. DIA is therefore more suitable for discovery and screening, while PRM is suited to targeted follow-up analysis.

 

2. Can PRM Replace Western Blot or ELISA?

PRM, Western blot, and ELISA provide different types of analytical evidence. PRM is a mass spectrometry-based targeted quantitative method and should not be considered a universal replacement for antibody-based methods.

 

3. Can PRM Be Used for Absolute Quantification?

Yes, when an appropriate quantitative design is used. Absolute quantification generally requires suitable internal standards, reference materials, calibration strategies, and target-specific method development.

 

Request a DIA+PRM Target Proteomics Project

If your study requires broad DIA quantitative screening followed by targeted PRM analysis, contact MtoZ Biolabs with your species, sample type, experimental groups, research objective, and candidate protein or peptide list if available.

 

MtoZ Biolabs can evaluate whether DIA, PRM, or an integrated DIA+PRM strategy is appropriate and confirm sample requirements and analytical scope before project initiation.

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

Related Services

Targeted Proteomics Service

Targeted Quantitative Proteomics Service

4D-PRM Target Proteomics Services

DIA Quantitative Proteomics Analysis Service

Targeted Mass Spectrometry Service