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Creative Proteomics offers aptamer-based proteomics profiling, combining SELEX and mass spectrometry for biomarker discovery and target identification.

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Aptamer-Based Proteomics Profiling Service

Scale your discovery with 11,000-plex protein profiling. Move beyond the limitations of traditional proteomics. Our high-plex aptamer-based platform delivers simultaneous quantification of over 11,000 proteins from a single, small-volume sample, unlocking unprecedented depth for biomarker and target discovery.

  • Unmatched Scale: Interrogate 11,000 proteins in one assay for a truly systems-level view of the proteome.
  • Superior Specificity: Aptamers provide high-affinity binding, enabling accurate detection of low-abundance and challenging targets.
  • Robust & Reproducible: Chemically synthesized reagents ensure exceptional batch-to-batch consistency and data reliability.
  • Streamlined Workflow: Achieve high-depth proteomic data faster and with less sample input.
Creative Proteomics’ aptamer-based proteomics profiling service.

What is Aptamer-Based Proteomics Profiling?

Aptamer-based proteomics profiling is a molecular detection and quantification technique that utilizes synthetic oligonucleotides, known as aptamers, to bind protein targets selectively. These aptamers are generated through Systematic Evolution of Ligands by Exponential Enrichment (SELEX), which allows the selection of molecules with high specificity and affinity toward target proteins. Unlike antibodies, aptamers are chemically synthesized, reducing batch-to-batch variability and ensuring consistent performance. The technology enables researchers to monitor hundreds to thousands of proteins in a single assay, providing a global view of the proteome.

High-plex aptamer-based proteomics allows simultaneous measurement of thousands of proteins in a single experiment. The technology preserves native protein conformations and post-translational modifications, providing biologically meaningful data. It is particularly effective for membrane proteins, low-abundance targets, and cell-surface markers that are challenging for conventional methods.

Why Choose Aptamers for Proteomics?

Aptamers possess several properties that make them particularly suitable for proteomic analysis:

Schematic of CELL-SELEX

Figure 1. Schematic representation of CELL-SELEX (Huang J, et al., 2021).

Key Technology for Aptamer-Based Proteomics Profiling

SELEX

SELEX provides the fundamental selection process. The laboratory performs standard SELEX for purified targets. The team employs Cell-SELEX for whole-cell targets. The group applies in vivo SELEX for tissue-directed selection when applicable. The platform includes microfluidic and automated SELEX variants for throughput and reproducibility. The laboratory implements counter-selection to remove non-specific binders. The scientists monitor enrichment across iterative rounds.

Next-generation sequencing

NGS quantifies sequence enrichment. Bioinformatics identifies candidate aptamer families. Motif analysis detects conserved structural elements. The computational pipeline estimates relative abundance and convergence. The team annotates potential off-target motifs. The data supports rational truncation and affinity maturation.

Target identification by mass spectrometry

Affinity pull-downs with candidate aptamers precede LC-MS/MS analysis. The proteomic workflow employs high-resolution instruments. Tandem mass spectrometry achieves peptide sequencing and protein identification. Target deconvolution uses label-free quantification or isobaric labeling when needed. The approach enables identification of post-translational modifications and interacting partners.

Assay development and orthogonal validation

The group develops orthogonal assays for confirmation. Flow cytometry, immunofluorescence, and targeted PRM validate localization and abundance. Functional assays examine biological relevance. The integrated pipeline ensures that candidate aptamers translate into usable reagents.

Compare Aptamer-Based Profiling with Mass Spectrometry Proteomics

Feature Aptamer-Based Profiling Mass Spectrometry Proteomics
Principle Uses short, single-stranded DNA or RNA molecules that bind targets with high specificity. Measures protein mass and fragments to identify and quantify proteins directly.
Target Knowledge Required Can discover unknown proteins; works with cell surfaces and complex samples. Hypothesis-free; no prior knowledge needed.
Sensitivity High affinity for low-abundance proteins; can detect rare targets on cell surfaces. High dynamic range but may miss extremely low-abundance proteins without enrichment.
Specificity Can distinguish closely related isoforms and conformations; chemical modifications improve selectivity. Very high specificity at peptide level; can detect sequence variants and modifications.
Throughput High; multiple aptamers can be screened simultaneously. High, but dependent on instrument time and sample preparation.
Post-Translational Modifications (PTMs) Indirect detection possible if aptamer binds modified sites, but not comprehensive. Excellent; can identify phosphorylation, acetylation, glycosylation, and other modifications.
Ease of Optimization Aptamers can be chemically modified and iteratively optimized in vitro. Optimization relies on instrument settings and sample prep; no reagent modification possible.
Sample Flexibility Works with purified proteins, cell surfaces, tissues, and complex mixtures. Works with diverse samples but may require enrichment for low-abundance targets.
Ideal Use Cases Biomarker discovery, receptor mapping, early-stage diagnostics, cell-type specific targets. Comprehensive proteome mapping, PTM analysis, interactome studies.

Workflow for Our Aptamer-Based Proteomics Profiling Service

Workflow for aptamer-based proteomics profiling service.

Applications of Aptamer-Based Proteomics Profiling

Sample Requirements

Sample Types Cell lines, primary cells, tissue samples (fresh or frozen), plasma, serum, or purified proteins. Fixed cells can also be used, but prior discussion is required.
Sample Quantity Typically, 1–5 million viable cells for cell-based selection; 100–200 µL of serum or plasma; 50–100 µg of purified protein. Exact amounts will be confirmed during project planning.
Sample Quality Cells should be viable and free from contamination. Tissues should be fresh or snap-frozen. Protein samples should be highly pure, with minimal degradation. High-quality input improves aptamer selection success.
Storage & Shipping Samples should be shipped on dry ice (for frozen tissues/proteins) or in temperature-controlled containers (for cells). Creative Proteomics provides detailed packing and shipping instructions.

Why Choose Creative Proteomics for Aptamer-Based Proteomics Profiling

FAQ

Q1: How does aptamer specificity compare to monoclonal antibodies?

A1: Aptamers can achieve high specificity comparable to monoclonal antibodies. Unlike antibodies, aptamers can be chemically optimized to reduce off-target interactions and can discriminate between highly similar protein isoforms or post-translationally modified variants.

Q2: Can aptamer-based profiling detect post-translational modifications (PTMs)?

A2: Yes. By combining aptamer enrichment with mass spectrometry, the method can identify PTMs such as phosphorylation, glycosylation, or acetylation. Aptamers can selectively capture proteins in their native state, preserving modification patterns for downstream analysis.

Q3: Are aptamers compatible with in vivo applications?

A3: Certain aptamers selected via in vivo SELEX can function within living organisms, targeting tissues or cell types in their native environment. Chemical modifications enhance stability and bioavailability for in vivo studies.

Q4: How does aptamer-based profiling integrate with other omics approaches?

A4: Aptamer-based proteomics complements transcriptomics, genomics, and metabolomics. For example, aptamer-enriched proteins can be subjected to mass spectrometry, providing proteomic data that integrates with gene expression profiles, facilitating multi-omics biomarker discovery and mechanistic studies.

Demo

Demo: Alkaline phosphatase ALPPL-2 is a novel pancreatic carcinoma-associated protein

Cell-SELEX based identification of aptamer SQ-2.

Figure 2. Cell-SELEX based identification of PDAC specific aptamer SQ-2 (Dua P, et al., 2013).

Case Study

Case: Aptamer-Based Proteomic Profiling Reveals Novel Candidate Biomarkers and Pathways in Cardiovascular Disease.

Abstract

Single-stranded DNA aptamers can bind proteins with high specificity and affinity. Aptamer-based multiplexed platforms enable high-throughput measurement of large numbers of low-abundance circulating proteins and thus complement traditional proteomic approaches when profiling perturbational or cohort studies. The authors aimed to assess whether an aptamer-based proteomic platform (measuring ~1,129 proteins) could detect early, dynamic protein changes after myocardial injury and identify candidate biomarkers and pathways relevant to cardiovascular disease. They also evaluated the platform's performance in epidemiologic cohorts and developed an orthogonal workflow integrating aptamer affinity capture with mass spectrometry for analytical validation.

Methods

  • Sample collection and processing: Venous blood was collected into anticoagulant tubes according to a standardized protocol. Plasma was separated by centrifugation within two hours of collection. Aliquots were stored at −80 °C until analysis.
  • Aptamer-based proteomic measurement: Plasma samples were analyzed using a high-plex aptamer-based proteomic assay targeting approximately 1,129 proteins.
  • Aptamer affinity enrichment and mass spectrometry validation: Bound proteins were eluted, denatured, reduced, alkylated, and digested with trypsin. Peptide mixtures were analyzed by liquid chromatography–tandem mass spectrometry (LC–MS/MS). Mass spectra were searched against a human protein database.
  • Analytical validation and orthogonal assays: Affinity and kinetic measurements were obtained for selected aptamers using surface-based binding assays. Concordance between aptamer-derived signals and orthogonal measurements was assessed.

Results

  • 217 proteins changed significantly after planned myocardial infarction in the derivation cohort; 79 were validated in the independent cohort. More than 85% of validated proteins were directionally consistent.  
  • Several proteins not previously linked to acute myocardial injury were identified (for example, Dickkopf-related protein 4 and cripto), with substantial early increases in circulation. A subset of proteins that rose within 1 hour after planned injury was also elevated in spontaneous myocardial infarction cases.
  • Analyses in the Framingham Heart Study found many proteins associated with the Framingham Risk Score and its components, demonstrating applicability in large cohort studies.
  • The authors successfully demonstrated a workflow that couples DNA-based immunoaffinity enrichment to LC-MS/MS, providing orthogonal analytical confirmation of aptamer targets.
Proteins increased at the stage of planned and spontaneous myocardial injury.

Figure 3. Proteins increased during planned and spontaneous myocardial injury.

MS verification of aptamer-protein binding.

Figure 4. Mass spectrometry verification of aptamer-protein binding.

Conclusion

The study demonstrates that aptamer-based proteomic profiling is a sensitive, high-throughput approach that measures>1,000 low-abundance analytes. It can identify early protein changes after acute cardiac injury, discover novel candidate biomarkers and pathways, and scale to large cohorts. Integrating aptamer affinity enrichment with mass spectrometry provides a practical route for target validation. The platform shows promise for biomarker discovery and translational cardiovascular research.

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