Stable Isotope Labeling

Stable isotope labeling is a cornerstone technique in structural biology, metabolomics, and proteomics, enabling precise tracking of molecular interactions, metabolic flux mapping, and protein structure resolution via NMR or mass spectrometry. This method is vital for studying drug-target binding, quantifying disease pathway dynamics, and validating biomarkers. High-quality labeling is essential to ensure data accuracy and reproducibility, as impurities or inconsistent efficiency can skew results in sensitive applications like protein folding studies. Rigorous quality control—from isotope purity validation to batch consistency—minimizes variability, supporting robust conclusions in peer-reviewed research.

High-purity labeling ensures reproducible data for sensitive applications like NMR or metabolic flux analysis. At Creative BioMart , rigorous QC protocols and ISO-certified workflows guarantee batch-to-batch consistency, minimizing experimental variability. Ready to accelerate your research? Explore our services or contact our experts today!

500+

Protein production projects

90%+

Success rate

95%+

Isotopic purity

c.a. 98%

Isotope enrichment

Background

Work Principle

Stable isotopes (e.g., ¹³C, ¹⁵N, ²H) are non-radioactive forms of elements that share nearly identical chemical properties with their natural counterparts but differ in neutron count. Unlike radioactive isotopes, they emit no radiation, making them safe for long-term experiments and ideal for tracing molecular dynamics in living systems.

Stable isotope labeling incorporates these isotopes into biomolecules (proteins, metabolites, nucleic acids) during synthesis or expression. For proteins, isotopes are introduced via metabolic labeling—cultivating cells in media enriched with isotope-labeled nutrients (e.g., ¹⁵N-ammonium chloride). For small molecules, chemical synthesis replaces specific atoms (e.g., ¹³C-glucose) to track metabolic pathways. The labeled molecules retain native functionality while enabling detection via NMR, mass spectrometry, or imaging.

Advantages

Non-Radioactive Safety

Stable isotopes (¹³C, ¹⁵N) eliminate radiation risks, enabling long-term in vivo studies and safe handling in academic or clinical labs.

Long-Term Experimental Stability

Isotope labels remain intact over months, ensuring data consistency in longitudinal studies like chronic disease modeling or ecosystem monitoring.

Analytical Technique Versatility

Compatible with NMR, LC-MS, IRMS, and imaging, isotopes adapt to diverse workflows—from structural biology to single-cell metabolomics.

High Sensitivity & Specificity

Isotopic mass shifts reduce background noise, enhancing detection limits for low-abundance biomarkers or transient metabolic intermediates.

Applications

Structural Resolution & Conformational Analysis

Stable isotope labeling services enable high-resolution structural studies of recombinant proteins (e.g., antibodies, viral antigens) via NMR or cryo-EM. They reveal folding pathways, ligand-binding dynamics, and aggregation-prone regions critical for therapeutic development.

Drug Target Validation & Mechanism Elucidation

These services support precise tracking of drug-protein interactions by labeling recombinant targets (e.g., kinases, GPCRs). Insights into binding kinetics and allosteric effects accelerate lead compound optimization.

Biosimilar & Biotherapeutic Quality Control

By labeling recombinant biosimilars (e.g., mAbs, cytokines), the service identifies structural deviations from originator drugs, ensuring batch consistency and compliance with regulatory standards (FDA/EMA).

Industrial Enzyme Engineering & Optimization

Labeling recombinant enzymes (e.g., cellulases, lipases) uncovers catalytic mechanisms and thermal stability bottlenecks, guiding modifications for biofuel production or waste bioremediation.

Service Details

Core Services

1	Uniform Labeling	Our service delivers uniform isotope labeling (¹³C, ¹⁵N) to enhance NMR and mass spectrometry analysis, offering unmatched clarity for protein folding, interaction studies, and dynamic behavior. Ideal for drug target validation and structural biology projects.
2	Amino-acid Selective Labeling	We specialize in selective amino acid labeling, reducing spectral complexity by focusing on key residues (e.g., lysine, methionine). Perfect for probing binding interfaces, post-translational modifications, or functional protein domains.
3	Segmental Labeling	Our segmental labeling service enables isotope incorporation into specific protein regions, streamlining studies of multi-domain systems or large complexes. Minimize costs while maximizing data relevance for antibody engineering or domain-focused research.
4	Methyl-specific Protonation	We optimize methyl-specific protonation (¹³CH₃) for deuterated proteins, enhancing NMR sensitivity in membrane proteins or macromolecular assemblies. Tailored for challenging targets requiring high-resolution structural data.
5	Site-specific Labeling	Our advanced site-specific labeling integrates isotopes at defined residues through genetic or chemical strategies, empowering detailed studies of enzyme mechanisms, ligand interactions, or catalytic site dynamics.
6	Structural Analysis	Our NMR laboratory is equipped with exceptional NMR instruments and to provide structural analysis on isotopic labeled proteins. This Accurate NMR structural analysis will be done after the appropriate isotope labeled proteins have been produced and purified on scale.

Service Delivery & Submission Guidelines

• Submission Requirements

• Sample Specifications
  • Provide purified protein/DNA samples (>90% purity) with detailed buffer composition and concentration.
  • Specify isotope preferences or allow us to source optimal labels.
• Pre-Submission Consultation
  • Share target protein size, domains, or residues for segmental/site-specific labeling.
  • Schedule a feasibility review with our team to align labeling methods with analytical tools (NMR, MS).

• Delivery Details

• Turnaround
  • Standard projects: 4–8 weeks (varies with labeling complexity).
  • Rush services: 3–4 weeks (additional fees apply).
• Data Delivery Formats
  • Receive raw data (NMR spectra, MS raw files) and analyzed results (PDF/Excel reports, structural models).
  • Optional formats: PDB files for structural biology or metabolic pathway maps.
• Post-Delivery Revisions
  • Request adjustments (e.g., isotopic enrichment levels) within 14 days of delivery.
  • Free minor revisions; major reprocessing incurs negotiated costs.

Why Choose Us?

Expertise in Advanced Protein & Isotope Solutions. With over one decade of specialization, we deliver precision in protein expression and isotope labeling for structural biology, metabolomics, and drug discovery. Our protocols align with NMR, MS, and cryo-EM workflows to meet diverse research demands.

Validated Industry Experience & Global Trust. Serving 500+ clients across academia and pharma, we’ve optimized scalable workflows for complex projects, from antibody engineering to metabolic flux studies. Our collaborations accelerate discoveries in oncology, enzymology, and environmental science.

Quality-Driven Processes & Certifications. ISO-certified labs ensure >95% product purity, validated through rigorous NMR, MS, and HPLC analyses. Batch-to-batch consistency and traceable documentation guarantee reliability for peer-reviewed publications and regulatory submissions.

Cost-Effective Solutions via Proprietary Innovation. Our patented labeling technologies reduce production costs by 30% without sacrificing accuracy. Flexible scaling—from mg to kg—supports budget-conscious projects while maintaining rapid turnaround times.

Customer-Centric Support & Satisfaction. Dedicated project managers provide 24/7 consultation, tailored troubleshooting, and milestone updates. We prioritize transparency, offering free feasibility assessments and post-delivery revisions to align outcomes with your goals.

Timely Delivery & End-to-End Reliability. Achieve 98% on-time delivery with priority scheduling for urgent projects. Post-service support includes data interpretation guides and follow-up experiments, ensuring seamless integration into your workflow.

Case Study

Case 1: Multiplex Glycoproteomic Analysis Using Stable Isotope Labeling

Research Background : Glycoprotein alterations are linked to diseases, making glycoproteomics vital for biomarker discovery. However, analyzing glycoproteins in biological samples is challenging due to low abundance and complexity.

Methods : Glycopeptides were isotopically labeled during cell culture using a combined SILAC and IDAWG approach, achieving high labeling efficiency (≥95%). Quantitation was validated by mixing cell lines in a 1:1:1:1 ratio and applying mathematical corrections. The method was applied to compare glycoproteomes of three breast cancer and one brain cancer cell line using LC-ESI-MS.

Results : The method demonstrated high labeling efficiency and reliable quantitation, identifying 264 glycopeptides across three replicates. Relative quantification of glycopeptides revealed up/down-regulation patterns among the cell lines.

Conclusion : This multiplex glycoproteomic approach enhances glycoproteomic analysis accuracy and applicability. It reduces analysis time and provides insights into glycosylation microheterogeneity, advancing breast cancer metastasis research.

Fig1. EICs of (a) light, (b) Gly-labeled, (c) SILAC-labeled, and (d) GlyProSILC-labeled glycopeptide AGPN(HexNAc2Hex6)GTLFVADAYK. (Jiang, et al ., 2025)

Case 2: SILAC-Labeled Antibodies for ADC Pharmacokinetics Evaluation

Research Background : Stable isotope labeling by amino acids in cell culture (SILAC) is a well-established technique in quantitative proteomics. It is also used to generate stable isotope-labeled (SIL) antibodies for internal standards in LC-MS/MS bioassays, improving quantitative robustness. Total antibody (TAb) measurement is crucial for evaluating the pharmacokinetics (PK) of antibody drug conjugate (ADC) candidates.

Methods : In this study, multiple SIL combinations of an antibody were used for cassette dosing and PK evaluation. SILAC-labeled ADC therapeutics were tested in preclinical studies to assess their impact on antibody PK. The study also involved conjugating SIL antibodies to cytotoxic payloads to create SIL ADCs and evaluating their PK in cynomolgus monkeys using cassette dosing.

Results : Preclinical studies showed that SILAC-labeled ADC therapeutics did not alter antibody PK. SIL antibodies exhibited comparable exposure to discretely administered unlabelled test articles in rats. Additionally, SIL ADCs yielded comparable PK results to discretely dosed unlabelled ADCs in cynomolgus monkeys.

Conclusion : Using SIL antibodies with a cassette dosing strategy increases PK screening throughput of ADC candidates in preclinical species. This approach also supports the responsible use of laboratory animals by adhering to the three-Rs principle (Replacement, Reduction, and Refinement).

Fig2. Peptide evaluation of SIL antibodies as a mixture. (Kumar, et al ., 2024)

Case 3: Nonhuman Sera as Internal Standards for LC-MS/MS Protein Quantitation

Research Background : Quantitation of proteins using LC-MS/MS is complex, with various options from label-free techniques to stable isotope-labeled (SIL) internal standards (ISs). SIL-ISs are considered the "gold standard" for quantitation due to their similar physiochemical properties to the analyte and ability to multiplex. However, purchasing SIL-ISs is resource-intensive, especially for screening large biomarker panels.

Methods : This study presents an alternative strategy using nonhuman sera as the IS for quantitating multiple human proteins. The effectiveness of this strategy was demonstrated using two high-abundance proteins (vitamin D binding protein [DBP] and albumin [ALB]) and extended to three cardiovascular disease risk markers (SERPING1, ANXA1, and PRKDC).

Results : The results showed highly specific, reproducible, and linear measurements of the proteins of interest. The precision and accuracy were comparable to the gold standard SIL-IS technique.

Conclusion : This approach offers a cost-effective solution for LC-MS/MS protein quantitation, though it may not be applicable to every protein. It provides a viable alternative for many proteins, reducing the resource intensity of using SIL-ISs.

Fig3. Chromatograms showing human peptides (first panel), FBS nonhuman surrogate IS (second panel), combined analytes (third panel), and comparison of unlabeled SERPING1 (125 fmol) vs SIL-IS (50 fmol). (Williams, et al ., 2024)

Customer Testimonials

"Uniform ¹⁵N/¹³C labeling of our mAb highlighted aggregation hotspots under stress conditions. Their GMP-compliant workflows accelerated analytical validation, directly supporting our FDA filing."

-Dr. James R., Head of Process Development | Global Biopharma Leader

"Methyl-specific labeling of ligninase revealed thermal stability bottlenecks via NMR. Their scalable protocols cut production costs by 25% while maintaining enzymatic activity."

-Dr. Viktor S., CTO | Biofuel Catalyst Startup

"Stable isotope-labeled calibrators for our cardiac biomarker assay ensured ISO compliance. Batch consistency eliminated regulatory rework, saving 3 months in timelines."

-Dr. Anika P., VP of Manufacturing | IVD Solutions Provider

"Amino acid-selective ¹⁵N labeling pinpointed our fusion protein’s receptor-binding interface. Data clarity exceeded industry benchmarks for patent submissions."

-Dr. Lena T., Senior Scientist | Oncology Therapeutics Firm

"Segmental isotope labeling of Fc domains validated structural equivalence to originators. Their team’s expertise prevented a 6-month delay in EMA submissions."

-Dr. Thomas K., Analytical Lead | Biosimilar Innovator

"¹³C-labeled allergenic proteins enhanced our ELISA sensitivity by 15x, critical for low-abundance allergen quantification in complex matrices."

-Dr. Clara M., QA Director | Global Food Ingredient Supplier

FAQs

• Q: What isotope types do you offer for protein labeling?

  A: We offer ¹³C, ¹⁵N, ²H, and combinations like ¹³C/¹⁵N for high-precision studies.

• Q: Can you perform custom labeling for unique research needs?

  A: Yes, we provide custom labeling solutions, including site-specific and amino-acid selective labeling.

• Q: Can your services support large-scale production needs?

  A: Absolutely, we offer scalable solutions from mg to kg, tailored to meet your specific project requirements.

• Q: How do you ensure the purity and consistency of labeled proteins?

  A: Our ISO-certified processes include rigorous NMR, MS, and HPLC analyses to ensure >95% purity and batch consistency.

• Q: Can you handle complex labeling requests for multi-domain proteins?

  A: Yes, our segmental labeling service enables precise labeling of specific protein regions, ideal for multi-domain studies.

References:

1. Jiang P.; et al. 4-plex quantitative glycoproteomics using glycan/protein-stable isotope labeling in cell culture. J Proteomics . 2025;310:105333.
2. Kumar V.; et al. Use of stable isotope labeled (SIL) antibodies in cassette dosing to improve pharmacokinetics screening efficiency of ADCs with novel cytotoxic payloads. Xenobiotica . 2024;54(8):502-510.
3. Williams G.; et al . Use of Nonhuman Sera as a Highly Cost-Effective Internal Standard for Quantitation of Multiple Human Proteins Using Species-Specific Tryptic Peptides: Applicability in Clinical LC-MS Analyses. J Proteome Res. 2024;23(8):3052-3063.