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PRM Targeted Proteomics

PRM Targeted Proteomics

Advanced 4D LC-MS/MS Platform for High Sensitivity and Selectivity
Targeted Quantification with Excellent Reproducibility
Broad Compatibility with Diverse Sample Types
Scalable Workflow for Multi-Sample and Multi-Batch Analysis

Technology Overview: Parallel Reaction Monitoring (PRM) for Targeted Proteomics

Parallel Reaction Monitoring (PRM) is a highly selective and sensitive targeted mass spectrometry technique designed for accurate quantification of predefined proteins or peptides. In PRM mode, selected precursor ions are fragmented, and all corresponding product ions are monitored simultaneously with high resolution and mass accuracy. This approach enables confident detection of low-abundance targets with excellent specificity and reproducibility, even in complex biological samples such as plasma, tissue, or cell lysates.

MetwareBio’s PRM-Based Targeted Proteomics Service is built on the Bruker timsTOF platform, equipped with Trapped Ion Mobility Spectrometry (TIMS) and the advanced prmPASEF acquisition mode. This powerful setup ensures highly efficient ion utilization, exceptional sensitivity, and accurate quantification of target peptides with outstanding reproducibility. With robust performance and high-throughput capability, the service is ideally suited for biomarker validation, drug target verification, pathway-specific analysis, and translational or clinical proteomics applications.

prm-PASEF workflow for targeted proteomics experiments (Lesur et al., 2021)

Why Choose Our PRM Proteomics Service

High Specificity and Selectivity
PRM monitors all fragment ions of each targeted precursor in high resolution, allowing accurate distinction of target peptides from background noise or closely related sequences—ensuring confident quantification in complex biological samples.
Ultra-Fast Acquisition with TIMS + PASEF
Powered by Bruker timsTOF HT and advanced TIMS-PASEF® technology, our platform enables rapid and high-resolution ion separation and acquisition, ensuring confident protein identification even in highly complex samples.
High Sensitivity, Accuracy, and Throughput
Powered by prmPASEF acquisition, PRM enables highly sensitive and precise quantification of low-abundance targets with minimal interference, supporting high-throughput validation of specific proteins across complex samples.
Outstanding Reproducibility for Targeted Quantification
With consistent and multiplexed monitoring of fragment ions for each target, PRM ensures exceptional reproducibility across replicates and sample batches—making it ideal for large-cohort studies, clinical validation, and translational research.
Customizable and Scalable Assay Design
Enables flexible panel development based on user-defined targets, supporting focused analysis of specific pathways, protein families, or clinically relevant biomarkers across diverse sample sets.
Multi-Omics Integration Ready
As a leading multi-omics CRO, MetwareBio offers not only advanced proteomics, but also fully integrated metabolomics, lipidomics, and transcriptomics services—enabling comprehensive multi-omics analysis and systems-level biological insights through a unified, end-to-end platform.
PRM Targeted Proteomics Project Workflow
1
Sample Shipment
2
Sample Preprocessing
3
Library Construction
4
Method Optimization
5
Targeted Detection
5
Data Analysis

Applications of PRM-Based Targeted Proteomics

Clinical and Translational Research

PRM is widely used in clinical proteomics for the sensitive and reproducible quantification of disease-associated proteins. It enables biomarker validation, therapeutic target verification, and longitudinal monitoring of protein expression in plasma, tissue, or FFPE samples—supporting diagnostic and precision medicine applications.

Pharmacology and Drug Development

In preclinical and translational drug studies, PRM offers high-precision quantification of drug targets, pharmacodynamic markers, and proteins involved in mechanisms of action or off-target effects, facilitating informed decision-making during compound screening and evaluation.

Animal and Plant Biology

PRM supports targeted protein quantification in model organisms and agricultural species, helping researchers investigate developmental pathways, stress responses, and hormone signaling. In crops and livestock, PRM aids in functional protein validation and trait-related biomarker discovery.

Microbial and Environmental Research

In microbial systems and environmental samples, PRM enables precise measurement of regulatory enzymes, virulence factors, and stress-related proteins, supporting studies in pathogenesis, bioremediation, and host–microbe interactions.

PRM Proteomics Sample Requirements

Sample Type Samples Recommended Sample Size Minimum Sample Size
Human/Animal Tissue Normal tissues (heart, liver, spleen, lungs, intestines, kidneys, etc.) 50mg 5mg
Fatty tissue 200mg 100mg
Brain tissue 50mg 5mg
Bone 1g 200mg
Hair 500mg 200mg
Skin 200mg 100mg
Plant Tissue Young tissue (young leaf, seedling, petal, etc.) 200mg 100mg
Mature tissue (root, stem, fruit, pericarp, etc.) 1g 500mg
Pollen 40mg 15mg
Liquid Samples Serum/Plasma (without removing high abundance proteins) 20μL 5μL
Serum/Plasma (remove high abundance proteins) 200μL 100μL
Joint fluid, Lymph fluid 200μL 100μL
Aqueous humor, Vitreous body 300μL 200μL
Cerebrospinal fluid 200μL 100μL
Ascites, Follicular fluid 100μL 50μL
Alveolar lavage fluid (BALF) 1ml 500μL
Amniotic fluid 1ml 500μL
Milk 20μL 5μL
Urine 10mL 5mL
Saliva (mammals) 1ml 500μL
Fermentation broth, Bacterial solution 10ml 5ml
Cellular supernatant 25mL 10ml
Exosome (sediment) 25μl 15μL
Microorganisms Bacteria 200mg 100mg
Fungi 300mg 150mg
Cells Primary Cells 3×10^6 1×10^6
Transmissible cells 2×10^6 1×10^6
Sperm, Platelets 2×10^7 1×10^7
Protein Protein 100μg 50μg
Biological duplicates: A minimum of 3 replicates is required; 3-6 replicates for animal samples; 6-10 for clinical samples.

 

Frequently Asked Questions about PRM Proteomics

What is PRM and how does it differ from DIA or DDA-based proteomics?

PRM (Parallel Reaction Monitoring) is a targeted mass spectrometry technique optimized for precise quantification of predefined peptides or proteins. Unlike DIA or DDA, which aim for broad proteome coverage, PRM provides higher selectivity and quantitative accuracy, making it ideal for validating candidate biomarkers or pathway-specific proteins.

How is the spectral library generated for PRM analysis?

To ensure accurate detection and quantification, we use DIA-based acquisition (diaPASEF) to generate high-quality spectral libraries. This approach ensures comprehensive peptide coverage, reproducible fragment ion patterns, and robust assay development for PRM.

How many targets can PRM monitor in a single run?

Our PRM workflow typically supports dozens to hundreds of peptides per run, depending on the complexity of the sample and retention time scheduling. We tailor assay design to balance multiplexing depth with signal quality.

Can PRM be used to validate targets identified from previous DIA or DDA studies?

Yes. PRM is particularly effective for validating candidate proteins identified in discovery-phase studies, including DIA or DDA. It offers higher quantitative precision and consistency across samples, making it ideal for verification and translational studies.

Can PRM analysis be performed on immunoprecipitated (IP) samples?

Yes. PRM is highly compatible with IP-based protein enrichment workflows. We recommend using at least 20 μL of magnetic bead pellet or 50 μL of IP eluate for optimal detection and quantification of target proteins.

Can PRM be applied to SDS-PAGE gel bands or gel strips?

Yes. We can analyze gel-excised protein bands or regions following SDS-PAGE separation. To assess feasibility, we require an image of the gel to evaluate target protein abundance and background complexity before proceeding.

Start Your Project

 

Reference

Lesur, A., Schmit, P. O., Bernardin, F., Letellier, E., Brehmer, S., Decker, J., & Dittmar, G. (2021). Highly Multiplexed Targeted Proteomics Acquisition on a TIMS-QTOF. Analytical chemistry, 93(3), 1383–1392.https://doi.org/10.1021/acs.analchem.0c03180

Next-Generation Omics Solutions:
Proteomics & Metabolomics

Have a project in mind? Tell us about your research, and our team will design a customized proteomics or metabolomics plan to support your goals.
Ready to get started? Submit your inquiry or contact us at support-global@metwarebio.com.
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