SILAC-Based Quantitative PTM Service

MtoZ Biolabs relies on high-resolution mass spectrometry platforms (including Orbitrap Fusion Lumos and Q Exactive HF) and an experienced analytical team to establish a standardized SILAC-Based Quantitative PTM Service that provides research institutes and pharmaceutical companies with an integrated solution covering isotopic labeling, protein extraction, modified peptide enrichment, quantitative analysis, and bioinformatics interpretation to help clients systematically analyze protein modification dynamics and signaling regulation.

 

Technical Principle

SILAC (Stable Isotope Labeling by Amino acids in Cell culture) is a cell culture-based quantitative proteomics method using stable isotope labeling. It enables accurate quantification of proteins and their post-translational modifications (PTMs) without disrupting physiological conditions. SILAC introduces light and heavy isotope-labeled amino acids (such as ¹³C₆-Lysine and ¹³C₆ ¹⁵N₄-Arginine) during cell culture so that newly synthesized proteins naturally contain mass differences, allowing quantitative comparison between samples. This strategy avoids errors caused by chemical derivatization, offering high reproducibility and minimal experimental bias. The labeling is completed at the initial sample preparation stage, avoiding uncertainty from later chemical reactions, making SILAC particularly suitable for dynamic PTM studies.

Analysis Workflow

1. SILAC Cell Labeling and Protein Preparation: Provide stable isotope amino acid labeling, cell culture, and quality verification services to ensure labeling efficiency meets experimental standards.

2. PTM Enrichment Analysis: For different modification types such as phosphorylation, acetylation, ubiquitination, and SUMOylation, IMAC, TiO₂, antibody-based, or chemical affinity enrichment strategies are applied.

3. High-Resolution Mass Spectrometry Detection: Use Orbitrap platforms for high-precision detection to capture modification peptide signals and achieve light/heavy isotope quantification.

4. Bioinformatics and Functional Annotation: Integrate differential analysis, pathway enrichment, and modification site network construction to reveal the functional significance of dynamic modification changes.

 

Figure 1. SILAC-Based Quantitative PTM Analysis

Service Advantages

1. High Physiological Relevance

SILAC labeling is completed during cell culture without chemical modification or in vitro reactions, avoiding non-physiological interference. The resulting data more accurately reflect intracellular protein and PTM dynamics, especially suitable for time-dependent signal regulation studies.

 

2. High Accuracy and Low Bias

Unlike chemical labeling methods, SILAC samples are labeled and cultured before mixing, minimizing batch variation and technical noise. This ensures the reproducibility and reliability of quantitative results.

 

3. Compatibility with Multiple PTM Types

The SILAC workflow developed by MtoZ Biolabs can flexibly accommodate various PTM types, including phosphorylation, acetylation, ubiquitination, SUMOylation, and methylation. Combined with specific enrichment technologies, it enables comprehensive multidimensional PTM analysis.

 

4. High-Sensitivity Mass Spectrometry Platforms

We utilize Orbitrap Fusion Lumos and Q Exactive HF systems to achieve high-resolution and wide dynamic range detection, ensuring high-confidence identification and quantification accuracy of modified peptides.

 

Applications

1. Signaling Pathway and Stress Response Studies: Analyze dynamic modification changes under external stimuli.

2. Disease Mechanism Exploration: Investigate PTM abnormalities in cancer, metabolic diseases, and neurodegenerative disorders.

3. Drug Mechanism Studies: Evaluate how candidate compounds regulate protein modifications and signaling pathways.

4. Systems Biology and Regulatory Network Construction: Build multi-modification regulation models to reveal complex biological control mechanisms.

 

FAQs

Q1: Is it applicable to all cell types?

A1: It is suitable for most adherent and suspension cell lines, but the cells must have sufficient growth capacity to complete labeling.

 

Q2: What is the typical project duration?

A2: Depending on sample type and analysis depth, the typical project requires 4–6 weeks, including mass spectrometry analysis and report generation.

 

Sample Submission Suggestions

1. Sample Type: Adherent or suspension cells; stable mammalian cell lines are recommended.

2. Sample Amount: At least 1×10⁷ cells per group to ensure sufficient protein yield.

3. Sample Condition: Frozen lysate or cell pellet; avoid repeated freeze-thaw cycles.

4. Culture Conditions: Provide information on the light/heavy amino acids used and the labeling duration.

5. Additional Information: Include experimental design, treatment conditions, and research objectives.

 

MtoZ Biolabs provides detailed SILAC labeling and sample preparation guidelines to ensure optimal results.

 

Deliverables

1. Complete experimental design and QC report

2. Quantitative results for proteins and modified peptides

3. Differential modification analysis and statistical report

4. Functional annotation, pathway enrichment, and visualized charts

5. Raw mass spectrometry data and processed standardized files

With advanced mass spectrometry platforms and a professional analytical team, MtoZ Biolabs delivers high-quality and reproducible SILAC-based quantitative PTM service. From isotope labeling to data interpretation, we offer comprehensive, rigorous support for your research. Contact MtoZ Biolabs today to begin your precise and quantitative PTM proteomics journey.