Protein Quantitation Assays Service

Protein quantitation can involve very different analytical questions, from measuring a defined target to comparing protein abundance across a larger sample set. The most appropriate assay depends on the number of proteins, sample type, expected abundance, study scale, and type of quantitative result required.

The Protein Quantitation Assays Service helps researchers select an appropriate analytical route while maintaining mass spectrometry as the primary platform for protein-specific and broader quantitative analysis.

Project Need	Recommended Approach
Quantify predefined proteins or peptides	PRM / MRM-SRM
Obtain absolute protein or peptide values	Stable isotope-assisted targeted LC-MS/MS
Compare multiple samples with chemical labeling	TMT / iTRAQ
Quantify compatible cultured-cell systems	SILAC
Compare flexible or larger sample sets	Label-Free Quantification
Improve quantitative consistency across larger studies	DIA-based Label-Free Quantification
Compare a small number of known proteins	Western Blot
Compare protein spot patterns or putative proteoform differences	2D-DIGE
Measure total protein concentration	BCA / Bradford

Service at MtoZ Biolabs

1. Mass Spectrometry-Based Protein Quantitation

Mass spectrometry is the core analytical platform within the Protein Quantitation Assays Service. LC-MS/MS workflows support protein- and peptide-specific quantitation across complex biological samples and can be adapted for focused targets, multiplex comparison, or broader protein analysis.

(1) Targeted Mass Spectrometry

PRM and MRM/SRM are suited to predefined proteins or peptides. Applications include candidate verification, targeted panels, treatment-response studies, and follow-up measurement after discovery proteomics.

Stable isotope-labeled internal standards and calibration strategies can be incorporated when absolute measurement or additional quantitative control is required.

Figure 1. Schematic Diagram of MRM/PRM

(2) Isotope Labeling-Based Quantitation

TMT and iTRAQ support multiplex relative protein quantitation across multiple samples or groups. TMT workflows can accommodate several multiplex formats, including higher-plex TMTpro designs, while iTRAQ commonly uses 4-plex and 8-plex formats.

SILAC provides metabolic isotope labeling for relative protein quantitation in compatible cultured-cell systems.

Figure 2. Schematic Diagram of TMT

(3) Label-Free Quantitation

Label-Free Quantification provides flexible protein comparison without chemical or metabolic labeling.

Label-free workflows can use DDA- or DIA-based acquisition. DDA is commonly used for discovery-oriented analysis, while DIA is well suited to studies requiring more consistent quantitative coverage across larger sample sets.

Figure 3. DDA and DIA Acquisition Principles

2. Complementary Protein Quantitation Assays

MtoZ Biolabs also provides complementary non-MS protein quantitation options when they better match the analytical question:

• Western Blot Quantitationfor relative analysis of a limited number of known proteins;
• 2D-DIGEfor differential protein spot analysis and comparison of putative proteoform patterns;
• BCA and Bradford Assaysfor total protein concentration measurement.

Differential spots obtained by 2D-DIGE can be selected for downstream mass spectrometry identification when required.

Applications

1. Proteomics Research

Quantitative analysis of changes in protein expression levels under different conditions.

 

2. Disease Diagnosis and Biomarker Research

Detection of specific protein concentration changes in biological samples for disease diagnosis and biomarker research.

 

3. Drug Development

Evaluation of the impact of drugs on protein expression levels for drug development and efficacy assessment.

 

4. Food and Agriculture Testing

Detection of protein content in food and agricultural products for quality control and safety assessment.

 

Why Choose MtoZ Biolabs?

1. Mass Spectrometry-Focused Analytical Capability

MtoZ Biolabs focuses on LC-MS/MS-based protein analysis, supporting targeted, isotope-labeled, and label-free quantitative workflows across diverse biological samples.

 

2. Project-Specific Method Selection

Target number, sample matrix, expected abundance, quantitative range, labeling requirements, and study scale are considered before the analytical workflow is finalized.

 

3. Relative and Absolute Quantitation Support

Protein quantitation projects can be designed for relative abundance comparison or stable isotope-assisted absolute measurement according to the required output.

 

4. Complementary Assay Options

Western blot, 2D-DIGE, BCA, and Bradford assays are also available when antibody-based, gel-based, or total protein measurement better fits the study.

 

5. Scientific Support

One-to-one technical support is available for assay selection, sample submission, workflow design, data analysis, and result interpretation.

Sample Submission Suggestions

Before starting a Protein Quantitation Assays Service project, please provide:

Information	Details
Species	Organism or model system
Sample Type	Cells, tissue, serum/plasma, protein extract, purified protein, or other matrix
Target Information	Known proteins or peptides, if applicable
Sample Number	Total number of samples
Group Design	Experimental groups and comparisons
Available Material	Sample amount or protein concentration
Sample Requirements	Samples should be kept intact and stable to avoid degradation or contamination
Reference Material	Available antibodies, standards, or labeled peptides, if applicable

Sample requirements can be reviewed before project initiation for limited material, complex matrices, or selected low-abundance targets.

FAQ

Q1. When should PRM or MRM/SRM be used?

PRM or MRM/SRM is appropriate when the proteins or peptides are already defined and focused quantitative measurement is required.

 

Q2. Can low-abundance proteins be quantified?

Selected low-abundance proteins can be quantified when the target, sample matrix, peptide response, and assay sensitivity are suitable. Sample enrichment or additional assay optimization may be required.

 

Q3. Can multiple proteins be quantified in one project?

Yes. Targeted MS, multiplex labeling, and broader quantitative workflows can support multiple proteins depending on the target number and analytical design.

 

Contact Us

Not sure which protein quantitation method fits your study? Share your sample type, target scope, sample number, and quantitative goal with MtoZ Biolabs. Our technical team can help recommend a suitable approach.

 

Free consultation is available.