SILAC (Stable Isotope Labeling by Amino Acids in Cell Culture)-Based Quantitative Service

What Is SILAC Quantitative Proteomics?

SILAC is a metabolic labeling-based quantitative proteomics method for relative protein abundance analysis. During cell culture, stable isotope-labeled amino acids are incorporated into cellular proteins, generating distinguishable Light and Heavy isotope signals between different experimental conditions. After labeled samples are mixed at defined ratios, LC-MS/MS analysis is performed, and protein abundance changes are quantified based on differences in corresponding peptide signals.

Figure 1. The Principle of SILAC 

SILAC quantitative proteomics is primarily applied to cultured cell models for comparative protein expression analysis, supporting studies of treatment responses, genetic regulation, and cellular state changes.

When This Service Is a Good Fit

How SILAC Could Help	Suitable Scenario
Identify Differentially Abundant Proteins	Compare protein abundance changes between different experimental conditions, such as control versus treatment groups, different cellular states, or different culture conditions.
Analyze Drug Response and Molecular Mechanisms	Analyze proteome changes induced by drug treatment, compound stimulation, or other cellular perturbations to identify affected proteins and biological pathways.
Study Genetic Regulation Effects	Investigate protein expression changes caused by gene knockout, knockdown, overexpression, or other genetic modifications.
Track Protein Complex Dynamics	Analyze changes in protein complex composition or associated protein abundance under different experimental conditions to study cellular regulation.

For research objects that cannot undergo SILAC metabolic labeling, such as tissues, blood, biofluids, or other non-cultured cell samples, TMT-based peptide-level chemical labeling strategies may be considered. MtoZ Biolabs also provides TMT quantitative proteomics services to support protein abundance comparison across diverse biological samples and large-scale quantitative proteomics studies.

Analysis Workflow

1. Sample Preparation and Quality Assessment

MtoZ Biolabs receives pre-labeled SILAC cell pellets, protein lysates, or gel samples and performs sample quality assessment before proteomics analysis.

2. Protein Extraction and Digestion

Protein extraction, reduction and alkylation, enzymatic digestion, and C18 desalting are performed to generate peptide samples suitable for LC-MS/MS analysis.

3. LC-MS/MS Data Acquisition

High-resolution mass spectrometry is used for DDA-based data acquisition to obtain peptide fragmentation information.

4. Database Searching and Quantification

MaxQuant or Proteome Discoverer is used for database searching, and SILAC isotope parameters are applied for protein identification and relative quantification.

5. Bioinformatics Analysis

Differential protein analysis, functional enrichment analysis, and protein-protein interaction analysis are performed to interpret protein expression changes.

Why Choose MtoZ Biolabs?

1. Accurate SILAC-Based Quantification

Stable isotope labeling enables Light/Heavy peptide comparison for reliable relative protein abundance analysis between experimental conditions.

2. Deep Proteome Profiling with High-Resolution MS

Orbitrap mass spectrometry supports deep protein identification, with routine cell samples enabling identification of thousands of proteins and mass accuracy below 5 ppm.

3. Standardized Proteomics Workflow

Integrated sample processing, LC-MS/MS analysis, quantitative analysis, and bioinformatics interpretation ensure reliable SILAC proteomics results.

4. Comprehensive Data Analysis Support

Provides protein identification, differential analysis, functional enrichment, PPI analysis, and customized bioinformatics solutions for biological interpretation.

Applications

1. Differential Protein Expression Analysis

Compare protein abundance changes between different cellular conditions, including control versus treatment groups, to identify differentially expressed proteins.

2. Drug Response and Mechanism Studies

Analyze proteome changes induced by drug treatment or cellular stimulation to identify affected proteins and biological pathways.

3. Protein Complex and Dynamic Proteomics Studies

Monitor changes in protein abundance within cellular complexes or under different cellular conditions to study dynamic regulation.

4. Protein Turnover Studies

Track protein synthesis and degradation dynamics using stable isotope labeling strategies in cultured cell models.

Sample Submission Requirements

Item	Requirement
Supported Sample Types	Pre-labeled SILAC cell pellets, SILAC-labeled cell lysates, labeled protein samples, or gel samples.
Labeling Requirements	Samples must have completed stable isotope labeling and be mixed according to the experimental design before submission.
Cell Types	Common cultured cell models, including adherent and suspension cells, are supported. Sample compatibility should be confirmed in advance.
Protein Sample Requirements	For solution samples, at least 20 μg total protein is recommended, with a protein concentration above 0.5 μg/μL.
Gel Sample Requirements	Gel bands should be visible by eye, and relevant experimental information should be provided.
Database Requirements	Species information and reference databases are required. UniProt and customer-provided FASTA databases are supported.
Shipping Requirements	Cell pellets and protein solutions should be stored appropriately and shipped on dry ice. Gel samples can be shipped according to sample conditions.

Deliverables

1. Protein and Peptide Identification Results

2. SILAC Quantification Results

3. Quality Control Results

4. Differential Protein Analysis

5. Functional Annotation and Enrichment Analysis

6. Protein-Protein Interaction (PPI) Analysis

7. Raw Mass Spectrometry Data Files

8. Final Analysis Report

FAQs

Q1. Does the SILAC service include cell culture and isotope labeling?

MtoZ Biolabs does not provide SILAC labeling during cell culture. Customers should complete cell culture, stable isotope labeling, and sample mixing before submitting samples for downstream proteomics analysis.

Q2. Can SILAC be used for protein interaction studies?

SILAC can be used to analyze changes in protein complex composition. However, the results reflect changes in protein abundance or complex composition and cannot independently prove direct in vivo protein interactions.

Q3. How long does a SILAC quantitative proteomics project usually take?

A typical SILAC quantitative proteomics project takes approximately 3–4 weeks. The actual timeline may vary depending on sample quality, sample preparation complexity, instrument scheduling, and customized bioinformatics requirements.

Start Your SILAC Quantitative Proteomics Project

Planning a SILAC quantitative proteomics study? Provide your cell type, labeling strategy, experimental design, sample information, and research objectives. Our technical team can evaluate sample compatibility, analysis workflow, and downstream bioinformatics options before project initiation.