Label-Based Protein Quantitative Service—iTRAQ, TMT, SILAC

Label-based quantitative proteomics is designed for studies in which multiple biological samples need to be compared within a coordinated quantitative workflow. By introducing chemical or metabolic labels before LC-MS/MS analysis, samples can be distinguished and quantified across predefined experimental groups.

MtoZ Biolabs supports label-based workflows for treatment comparisons, time-course studies, gene perturbation experiments, disease models, and other projects where relative protein abundance needs to be evaluated across clearly defined conditions.

Service at MtoZ Biolabs

MtoZ Biolabs provides TMT, iTRAQ, and SILAC quantitative proteomics services, covering labeling strategy design, sample preparation, high-resolution LC-MS/MS acquisition, protein quantification, statistical analysis, and downstream biological interpretation.

Strategy	Available Options	Typical Project Fit
TMT	2-, 4-, 6-, 10-plex	Multiplex comparison across predefined groups
iTRAQ	4-plex and 8-plex	Multi-group relative protein quantification
SILAC	Study-specific metabolic labeling	Compatible cultured-cell experiments

Label-based quantitative workflows are performed using high-resolution mass spectrometry coupled with advanced LC systems for protein identification and relative quantitative analysis.

Typical outputs can include protein identification, quantitative matrices, differential protein analysis, quality assessment, clustering, functional annotation, pathway analysis, raw LC-MS/MS data, and a final project report.

Technical Principles

1. TMT

Tandem Mass Tags (TMT) are isobaric chemical labels applied to peptides after protein digestion. Differently labeled samples are pooled before LC-MS/MS analysis, and relative abundance is determined from reporter-ion signals generated during tandem mass spectrometry.

Key strengths

• Supports multiplex comparison across multiple samples

• Enables coordinated analysis of predefined experimental groups

• Reduces the number of separate LC-MS/MS runs required for grouped studies

• Well suited to structured comparative proteomics designs

Applications

TMT is commonly used for treatment-response studies, time-course experiments, disease-model comparisons, gene perturbation studies, and other projects involving several predefined biological groups.

Figure 1. Schematic Diagram of TMT

2. iTRAQ

iTRAQ also uses isobaric chemical labeling to compare relative protein abundance across multiple samples within a shared LC-MS/MS workflow.

Key strengths

• Supports simultaneous comparison across multiple groups

• Suitable for structured differential protein analysis

• Allows labeled samples to be pooled before LC-MS/MS acquisition

• Provides a practical option for multi-group relative quantification

Applications

iTRAQ can support differential protein screening, candidate prioritization, treatment comparisons, and studies involving several defined sample groups.

 

3. SILAC

Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) introduces isotopically labeled amino acids during cell growth. Proteins incorporate the labeled amino acids during synthesis, allowing differently labeled cell populations to be distinguished by mass spectrometry.

Key strengths

• Labeling occurs before protein extraction

• Samples can be combined early in the analytical workflow

• Reduces variation introduced during downstream processing

• Well suited to controlled cell-based experiments

Applications

SILAC is particularly useful for compatible cultured-cell systems in cell signaling studies, treatment-response experiments, gene perturbation, protein turnover research, and other applications where metabolic labeling can be incorporated into the experimental design. For non-cultured samples, chemical labeling or label-free quantitative workflows are generally more suitable.

Figure 2. Schematic Diagram of SILAC

Why Choose MtoZ Biolabs?

1. Flexible Labeling Strategies

TMT, iTRAQ, and SILAC provide complementary options for chemical and metabolic labeling across different experimental designs.

 

2. High-Resolution LC-MS/MS

Label-based workflows are supported by high-resolution LC-MS/MS for protein identification and relative quantitative analysis across complex biological samples.

 

3. Integrated Quantitative Analysis

Protein identification, quantitative comparison, statistical analysis, and downstream biological interpretation can be included within the same project.

 

4. Study-Specific Workflow Design

Sample type, group structure, biological replicates, labeling format, and analytical goals are considered before the workflow is finalized.

 

5. Scientific Support

Technical support is available for labeling strategy selection, group allocation, sample preparation, and interpretation of quantitative results.

 

FAQ

Q1: How should I choose between TMT, iTRAQ, and SILAC?

TMT and iTRAQ are chemical labeling approaches suited to predefined sample groups. SILAC is designed for compatible cultured-cell experiments where metabolic labeling can be incorporated during cell growth.

 

Q2: Can SILAC be used for tissue or biofluid samples?

SILAC is primarily used with compatible cultured-cell systems. Tissue, serum, plasma, and other non-cultured samples are generally better suited to TMT, iTRAQ, Label-Free, or DIA workflows.

 

Q3: What if my sample number does not fit a fixed labeling format?

For studies requiring greater flexibility in sample number, MtoZ Biolabs also provides Label-Free and DIA quantitative proteomics services.

 

Start Your Project with MtoZ Biolabs

Choosing the right labeling strategy starts with the sample type and group design. Share your sample number, experimental groups, biological replicates, and research goal with MtoZ Biolabs, and our technical team can help evaluate a suitable TMT, iTRAQ, or SILAC workflow.

Free consultation is available.

 

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