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PEPperCHIP® Custom Peptide Microarrays

Fully customizable peptide microarrays for high-resolution antibody characterization, from single antigens to complete viral proteomes.

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4.5k
Peptides / cm²
1 AA
Shift resolution
5-6 weeks
Delivery time
ISO 9001
Certified production
PEPTIDE MICROARRAYS IN A NUTSHELL

A powerful tool for high-resolution epitope mapping

Single amino
acid resolution
Resolve antibody-peptide interactions at residue level using large libraries of highly overlapping peptides.
Linear and conformational epitope analysis
Map linear or conformational epitopes by screening linear or special cyclic constrained peptides.
Scalable
immunoassay format
Detect specificity, off-target binding, and cross-reactivity across thousands of peptides in one experiment using a standard immunoassay workflow

HOW PEPTIDE MICROARRAYS WORK

A new way to explore proteins: How peptide microarrays work

PEPperCHIP® microarrays allow you to examine how individual amino acids within a protein sequence contribute to antibody binding.
By converting the sequence into a series of peptides that overlap with a single-amino-acid shift, binding can be resolved down to individual residues.

PROJECT WORKFLOW

Get your custom microarray in 3 simple steps

From initial inquiry to delivered product in 5-6 weeks. Here’s a quick walktrhough:
Step 1: Tell us what you need
Submit your protein sequences or research questions through our online form. Working with a pathogen proteome? Optimizing a therapeutic antibody? Profiling patient sera? Let us know what you're trying to accomplish.
If you’re uncertain about what you need, our specialists help you design the optimal library based on your research goals. Free consultation included with every project.
Step 2: We design your array together
Based on your sequences and goals, we create an initial microarray layout. This includes your custom library of maximally overlapping peptides (typically 15-mers with 14 amino acid overlap), plus optimized control peptides matched to your samples.
You review the design with your dedicated project manager. Need adjustments? Want to add more targets or change the overlap? We refine it together until it's exactly what you need.
Step 3: We print and deliver your custom microarray
Once you approve the design, production begins. Your custom microarray is produced using our laser-printing technology under ISO 9001 quality control. Every batch undergoes rigorous QC testing before shipment.
You receive: your custom microarray ready for use, detailed peptide location maps, and complete immunoassay protocols. If you're using PEPperMAP® Service, your microarray goes straight to our service lab. Just ship your samples and we handle the rest.

FLEXIBLE SOLUTIONS

Choose how you get your data

Whether you prefer hands-on control or full service support, you get the same expert guidance and quality microarrays. The difference is who handles the immunoassays and data analysis.

DIY Microarray Kit

What you get:
  • Free project consultation and array design
  • PEPperCHIP® Custom Peptide Microarray ready for use
  • Detailed peptide maps and protocols
  • Technical support from our team of scientists
You handle:
  • Sample preparation and immunoassay
  • Data acquisition (requires microarray scanner)
  • Data analysis and interpretation
Ideal for

Researchers with samples that cannot be shipped out or those who want to have full experimental control, teams with existing microarray analysis infrastructure.

PEPperMAP® Service

What you get:
  • Free project consultation and array design
  • PEPperCHIP® Custom Peptide Microarray
  • Complete immunoassay processing of your samples
  • Professional data acquisition and analysis
  • Full scientific report with visualizations
  • Dedicated project management
You handle:
  • Sample preparation and shipment to our facility
Ideal for

First-time peptide microarray users, labs without scanner access, researchers who prefer publication-ready data packages

Not sure which solution is best for you? We can help.

Start the conversation

How it works

STEP 1

Design Your Library

Send us your target sequences, or talk 
to our scientists for library design support (substitiution matrix, PTMs, or random peptides

STEP 3

Design Your Library

Send us your target sequences, or talk 
to our scientists for library design support (substitiution matrix, PTMs, or random peptides

STEP 2

Microarray Production

Peptides are synthesized with our laser printing platform following ISO 9001 certified quality standards. Chips are ready in 5-6 weeks

Choose how you get your data

DIY Microarray Kit

  • Wet-lab assay in your own facility (~3h hands-on; overnight incubation)
  • We provide immunoassay accessories and reagents,
in addition to the microarrays and analysis guide
  • Ideal if you have scanner access and prefer full control
Request Kit Quote

PEPperMAP® Service

  • We perform immunoassays, scanning, and data analysis
  • Detailed report with binding profiles and heatmaps
  • Recommended for high-throughput or complex projects
Discuss Your Project
RESEARCH QUESTIONS ANSWERED

See PEPperCHIP® Custom Peptide Microarrays in action

Take a closer look at some of our customers' most recent publications, and learn more about how they used PEPperCHIP® Custom Peptide Microarrays in their research.

PTM Characterization
Which citrullinated sites are targeted in rheumatoid arthritis?
Mapping 14,000+ citrullination sites with mass spectrometry and validating with peptide microarrays showed RA synovial fluid contains antibodies targeting PADI4-mediated citrullination of histones and non-histone proteins, connecting citrullination patterns to disease-specific immune profiles.
Rebak AS et al., 2024 ↗​
Anti-Drug Antibody Mapping
Which epitopes drive anti-drug antibody responses to therapeutic antibodies?
Peptide microarrays revealed pre-existing antibodies targeting a specific sequence motif in an anti-VEGF-A scFv antibody, detected in a large fraction of healthy donors, linking epitope-specific immunity to rare adverse immune events.
Karle AC et al., 2023 (Novartis) ↗​
Variant response
Does my vaccine strategy target the right epitopes for cross-variant protection?
Profiling SARS-CoV-2 spike variants using cyclic peptide microarrays showed heterologous vaccination uniquely targets conserved SD2/HR2 domains, functionally critical regions missed by single-variant approaches, explaining increased cross-variant neutralization breadth.
Frische A et al., 2024 ↗​
Melanoma
How do I identify resistance mechanisms to anti-VEGF therapy?
Epitope mapping validated anti-Galectin-1 antibody specificity in melanoma resistant to bevacizumab, confirming Gal1 as a compensatory angiogenesis factor and potential therapeutic target for overcoming anti-VEGF resistance.
Bannoud N et al., 2023 ↗​
PRODUCT DETAILS

Good to know

Key specifications

Scanner compatibility
All scanners that are compatible with 75 × 25 mm (3 × 1 in) microscope slides can be used. Recommended scanning resolution: 20µm or higher.
Standard: 75 × 25 mm slide (up to max. 50,000 unique peptides)
Proteinogenic and non-natural amino acids, and various modifications such as citrullination and phosphorylation. See full list.

Resources

PEPperCHIP® Immunoassay Protocol

Quick Start Guide

Behind the scenes:
How peptide microarrays are made

Have a sequence in mind?

Brainstorm your next project with us.
Our scientists will review your target and recommend the optimal peptide library—no obligation.
Start the conversation

Frequently Asked Questions

Before you get started

How long does it take to produce one custom peptide microarray?
Array production typically takes 4-5 weeks including comprehensive quality control steps. Details about the process of peptide array production can be found here.

Some. In addition to all 20 proteinogenic amino acids, we can also synthesize a range of D-amino acids, citrullinated, methylated, and phosphorylated peptides. You can find a complete list of available amino acids and monomers here.

PEPperCHIP® Peptide Microarrays should be stored at 4°C in the dark to ensure optimal stability. When handled properly, arrays remain stable for months. For maximum shelf life, we recommend storage under inert gas atmosphere when possible.
While arrays can theoretically be stripped and reused, stripping efficiency depends on your specific samples and assays. Since we can print multiple array copies per chip, we recommend using fresh arrays for each experiment to ensure optimal and consistent results.
We employ rigorous quality control including double coupling steps for quantitative yields, capping of unreacted amino groups, and comprehensive testing with reference peptides using HPLC and mass spectrometry. Our ISO 9001 certified process minimizes side reactions and ensures high-quality peptide synthesis.

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