LC-MS/MS MRM Analysis Service

What Is MRM-Based Targeted Proteomics?

MRM (Multiple Reaction Monitoring) is a targeted mass spectrometry-based quantitative technique performed on triple quadrupole mass spectrometers, also known as SRM (Selected Reaction Monitoring).

Unlike discovery-based proteomics approaches such as DDA or DIA, MRM/SRM is not designed for large-scale screening of unknown proteins. Instead, target proteins are predefined according to the research objectives, and specific signature peptides are selected for targeted quantitative analysis.

During MRM/SRM analysis:

• The Q1 quadrupole selects the target precursor ion;
• The Q2 quadrupole generates fragment ions through collision-induced dissociation (CID);
• The Q3 quadrupole selects specific product ions;
• The combination of precursor and product ions forms a specific transition for targeted signal acquisition and quantification.

 

Boja E S. et al. The Korean Journal of Laboratory Medicine. 2011.

Figure 1. The Principle of MRM/SRM

By monitoring predefined transitions, MRM/SRM reduces background interference in complex biological samples and improves the selectivity, sensitivity, and reproducibility of target protein quantification.

When This Service Is a Good Fit

1. Biomarker Candidate Validation

MRM/SRM can be used to validate candidate proteins identified from discovery-stage proteomics studies and perform targeted measurement across multiple independent samples.

2. Absolute Protein or Peptide Quantification

By incorporating stable isotope-labeled peptides (SIS peptides), MRM/SRM enables concentration measurement of selected proteins or signature peptides.

3. Site-Specific Quantification of Post-Translational Modifications (PTMs)

MRM/SRM can be applied for targeted quantification of predefined modified peptides, including phosphorylation and ubiquitination sites.

4. Large-Scale Sample Cohort Validation

MRM/SRM is suitable for studies requiring consistent and accurate quantification of a limited number of target proteins across multiple samples and experimental batches.

MRM/SRM is most suitable for hypothesis-driven studies with predefined targets. For projects involving unknown protein discovery or comprehensive proteome profiling, discovery-based approaches such as DDA or DIA proteomics may be more appropriate.

Service at MtoZ Biolabs

MtoZ Biolabs provides LC-MS/MS-based targeted proteomics quantification services and selects appropriate targeted MS strategies, including MRM/SRM or PRM workflows, according to research objectives, sample characteristics, and quantitative requirements.

For projects requiring targeted protein quantification with higher-resolution MS information or more flexible data analysis capabilities, PRM-based targeted proteomics using Orbitrap mass spectrometry can be considered.

By selecting appropriate targeted MS strategies based on sample characteristics, target protein abundance, and research objectives, MtoZ Biolabs supports biomarker validation, targeted protein measurement, and quantitative proteomics studies.

Analysis Workflow

1. Target Protein and Peptide Selection

Based on target protein information, sequence characteristics, and research objectives, suitable signature peptides are selected and targeted assay strategies are designed.

2. Sample Preparation and Peptide Generation

Biological samples undergo protein extraction, reduction and alkylation, enzymatic digestion, and desalting to generate peptide samples suitable for LC-MS/MS analysis.

3. Targeted LC-MS/MS Acquisition

MRM/SRM targeted acquisition is performed using triple quadrupole mass spectrometry by monitoring precursor-product ion transitions of target peptides for selective protein detection.

4. Quantitative Data Analysis

Target proteins are identified and quantified based on peptide chromatographic responses and MS signal intensity, supporting relative and absolute quantification analysis.

Service Advantages

1. High Sensitivity

MRM/SRM selectively monitors specific transitions of target peptides, reducing background interference in complex samples and improving the detection capability of low-abundance target proteins.

2. Excellent Reproducibility

The standardized targeted acquisition workflow and stable MS detection strategy enable consistent quantitative performance across different samples and batches, supporting large-scale validation studies.

3. High Accuracy

Signature peptide selection, transition optimization, and isotope-labeled internal standards improve the reliability and accuracy of target protein or peptide quantification.

4. High Throughput

MRM/SRM enables multiplexed detection of predefined target proteins and supports parallel quantitative analysis across large numbers of samples.

Sample Submission Requirements

Item	Requirement
Sample Type	Supports conventional biological samples for SRM targeted quantification. Target protein information, such as protein ID and corresponding amino acid sequence, should be provided for signature peptide selection and assay evaluation.
Sample Amount	Protein solution samples should contain at least 40 μg total protein with a concentration above 0.5 μg/μL. Specific sample requirements may vary depending on target protein abundance, sample type, and experimental design.
Sample Storage and Transportation	Original samples should be shipped on dry ice. Protein solution samples should avoid high salt concentrations and detergents that may interfere with enzymatic digestion and LC-MS/MS analysis.

Samples with extremely low target protein abundance, severe degradation, or insufficient information for reliable signature peptide selection require feasibility evaluation before project initiation.

FAQs

Q1: Is target protein information required before starting an SRM project?

Yes. SRM is a targeted mass spectrometry approach that requires predefined target information for signature peptide selection and assay design. Researchers are recommended to provide target protein names, UniProt IDs, species information, and research objectives for peptide suitability evaluation.

Q2: Does SRM measure intact proteins or peptides?

SRM typically follows a bottom-up proteomics strategy, where proteins are enzymatically digested into peptides before MS analysis. The detected signature peptides serve as surrogate measurements for the corresponding proteins.

Q3: Are synthetic standard peptides required for SRM analysis?

Not always. Relative quantification studies can be performed by comparing changes in target peptide signals between experimental groups. Stable isotope-labeled standard peptides are typically required for absolute quantification or improved peptide confirmation.

Q4: How can I determine whether a target protein is suitable for SRM analysis?

SRM assay feasibility depends on factors including protein sequence characteristics, availability of suitable signature peptides, target protein abundance, and sample matrix complexity. Some low-abundance or challenging proteins require feasibility assessment before analysis.

Q5: Is SRM suitable for unknown protein discovery?

No. SRM requires predefined target proteins and is primarily used for targeted quantification and candidate biomarker validation. Discovery approaches such as DDA or DIA proteomics are more suitable for large-scale protein profiling.

Q6: Can SRM results demonstrate protein functional changes?

SRM primarily provides quantitative information on target proteins or peptides and can reflect changes in protein abundance or modification levels. However, it does not directly demonstrate protein function, protein interactions, or biological causality, which require additional validation approaches.

Contact Us

MtoZ Biolabs provides LC-MS/MS-based MRM/SRM targeted proteomics quantification services supporting biomarker validation, targeted protein measurement, relative quantification, and absolute quantification studies.

Contact our scientific team with your target protein information, sample type, and research objectives. We will help design an appropriate targeted mass spectrometry strategy for your project.

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

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