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Infectious Diseases & Pathogen Profiling

Characterize pathogen-specific antibody responses at epitope resolution. Identify infection signatures, discover diagnostic biomarkers, assess population immunity, and rapidly profile emerging pathogen responses.
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What peptide microarrays enable

Decode antibody responses to pathogens

Understanding infectious disease immunity requires more than detecting whether antibodies bind a pathogen. Peptide microarrays reveal exactly where antibodies bind, enabling researchers to identify immunodominant epitopes, track variant recognition, and discover serological biomarkers.

Table of Contents

Identify infection-specific signatures

Distinguish acute infection from past exposure and differentiate between related pathogens or serotypes.

Profile responses against complete pathogen proteomes

Test thousands of peptides covering viral, bacterial, fungal, or parasitic antigens to map antibody responses during infection.

Differentiate between related strains or serotypes

Identify strain-specific versus conserved responses to distinguish closely related pathogens that cross-react in traditional assays.

Correlate immune patterns with disease outcomes

Map which antibody profiles associate with disease severity, recovery, or chronic infection across patient cohorts.

Discover diagnostic & prognostic antibody signatures

Analyze antibody profiles across patient cohorts to identify immune patterns associated with infection outcomes.

Compare immune responses across cohorts

Detect epitope-level patterns associated with disease severity or recovery.

Validate biomarkers across diverse populations

Confirm epitope-specific signatures hold across demographics, disease stages, and co-infections.

Support diagnostic assay development

Prioritize epitopes suitable for next-generation serological tests with high specificity and sensitivity.

Profile population immunity & exposure history

Assess seroprevalence in communities to understand population-level immunity and infection history.

Investigate immune escape mechanisms

Detect mutations that disrupt antibody binding.

Evaluate herd immunity for outbreak preparedness

Map antibody prevalence to assess immunity gaps and guide vaccination strategies.

Rapidly profile responses to emerging pathogens

Fast array design-to-assay turnaround lets you characterize immune responses before established assays exist.

Research questions answered

How researchers use peptide microarrays in infectious disease studies

Epitope-level profiling answers questions that shape outbreak response, diagnostic development, and immunity assessment. Here’s how researchers use peptide microarrays to understand pathogen-specific immune responses.

Vaccine optimization
Are conserved vaccine targets actually recognized during natural infection?
Peptide microarray screening of 128 overlapping peptides across 494 P. falciparum MSP2 variants revealed that conserved N- and C-terminal domains (assumed ideal vaccine targets) are rarely recognized during natural infection, redirecting vaccine design toward naturally immunodominant variable regions.
Zerebinski J et al., 2024 ↗​
Diagnostic discovery
Which epitopes are causing cross-reactivity in my diagnostic assay?
Mapping 375 overlapping peptides from Leishmania infantum NTPDase2 using peptide microarrays pinpointed four cross-reactive epitopes responsible for Chagas false positives. Removing these regions from the diagnostic antigen improved accuracy to 93%, eliminating cross-reactivity.
Castro RB et al., 2024 ↗​
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 ↗​
How it works

Identify, monitor and compare pathogen-specific antibody profiles with a single tool

Understand which pathogen proteins trigger antibody responses and identify their unique epitope signatures using a simple workflow.
Method comparison

Serological methods for pathogen profiling compared

Serological samples can be complex. Your analysis workflow shouldn’t have to be. Infectious disease research often relies on established serological methods to detect antibodies against pathogens. Peptide microarrays complement these approaches by revealing which epitopes antibodies recognize, adding epitope-level resolution to your data.

PEPperCHIP® Peptide Microarrays

ELISA

Multiplex Bead Assays (Luminex)

Protein Microarrays

Neutralization Assays
Typical question Which exact epitopes do antibodies recognize? Are antibodies present against this antigen? How strong are the antibody responses to multiple antigens? Which proteins are the antibodies recognizing? Do antibodies block infection?
Resolution Single amino acid Single amino acid Antigen-level Protein-level Functional
Antigen coverage per run Complete proteomes (≤45K peptides) Selected antigens 10-100 antigens ≤~20K proteins Single pathogen strain
Sample throughput Medium - high High High Low - medium Low (complex, time-intensive)
Best for Epitope mapping, diagnostic discovery, strain comparison Routine screening, quantification Multi-pathogen panels, seroprevalence studies Antigen discovery, protein-interaction profiling Functional immunity, vaccine efficacy studies

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

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Specialized capability

Profiling immune responses to bacteria?

Our peptidoglycan microarray is the first and only tool for mapping muropeptide-specific antibody recognition of bacterial cell wall antigens at scale. Profile immune responses across bacterial species to understand infection and microbiome immunity.
  • Distinguish commensal vs. pathogenic bacterial immunity
  • Map microbiome-associated antibody signatures
  • Support vaccine development and infection diagnostics
Discover our peptidoglycan array
PROJECT WORKFLOW

From pathogen sequence to antibody fingerprint

Pathogen profiling studies follow a straightforward workflow. Experiments can be performed in your own lab or through our PEPperMAP® service.

1

Target definition & library design

~1–2 days

PEPperPRINT

Design the microarray
We design the peptide library based on your target sequences and research objectives, then confirm the layout before production begins.

You

Define your question
Provide your research question and antigen sequence (FASTA or UniProt ID). We handle everything from here.
2

Microarray production

~5–6 weeks

PEPperPRINT

Synthesize & forward
We produce the microarray and run quality controls, then send them directly to our service labs.

You

Ship your sample
Send us your sample. We handle the rest.
⚠ ☣
Note: Infectious samples need to be heat-inactivated prior to shipping
3

Immunoassay

2 days

PEPperPRINT

Run the assay
We run the fluorescence-based immunoassay with your samples and scan the microarray to collect data.
View example scan output

You

Sit tight
Nothing required at this stage. If requested, we can send you the resulting scans at this point, though we usually send everything together with the report.
4

Data & analysis

~1-2 weeks

PEPperPRINT

Deliver your report
We analyze the scans data and deliver a full written report with annotated scans, intensity plots, and interpreted data.
View sample report

You

Receive your report
Your full analysis report is delivered digitally, ready to share with your team or include in a publication.
1

Target definition & library design

~1–2 days

PEPperPRINT

Design the microarray
We design the peptide library based on your target sequences and research objectives, then confirm the layout before production begins.

You

Define your question
Provide your research question and antigen sequence. Let us know if you’ll be needing additional accessories and reagents for running the assays.
2

Microarray production

~5–6 weeks

PEPperPRINT

Synthesize & ship
We produce the microarray and run quality controls. Then, we ship it to your facility.

You

Await delivery
Your microarray ships directly to your lab. Prepare your sample and reagents in the meantime.
3

Immunoassay

2 days

PEPperPRINT

Protocol support
We're on standby for protocol guidance and troubleshooting while you run the assay in your own lab.

You

Run the assay
Perform the immunoassay in your lab following our protocol. Contact us anytime for support.
4

Data & analysis

~1-2 weeks

PEPperPRINT

Analysis support
We're available for data interpretation support and can review your findings on request.

You

Analyse your data
Use our documentation and recommended analysis tools to interpret your results. We're on hand if you need us.
View example output
Related applications

Beyond pathogen profiling

Immune profiling extends across multiple research contexts. Here's where infectious disease researchers often go next:
Vaccines & Therapeutic Immunogenicity Profiling
Profile immune responses for vaccine optimization, anti-drug antibody detection, and immunotherapy development across preclinical to clinical stages.
Explore application →
Antibody Research & Epitope Mapping
Map binding sites, detect cross-reactivity, and identify critical residues for therapeutic antibody characterization and validation.
Explore application →
Autoimmune & Neurodegenerative Disease
Identify disease-specific autoantibody signatures, map autoantigens, and discover biomarkers for diagnostic development and patient stratification.
Explore capability →

Mapping antibody responses to pathogens?

Peptide microarrays can help you map antibody responses, identify pathogen epitopes, and uncover diagnostic biomarkers.
Not sure if this approach fits your study design? Let’s talk it through.
I'm interested
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Frequently Asked Questions

Before you get started

What exactly is pathogen profiling?
A pathogen profile in this context is a snapshot of unique antibody responses following exposure to a specific pathogen. To this end, we use a peptide scanning approach using a fluorescence-based immunoassay. We convert your pathogen antigens or proteome into overlapping peptides on a chip, incubate it with your sample, stain it with a secondary antibody, and identify the pathogen- (and disease-) specific epitope signatures by quantifying fluorescent signals of each peptide on the array.
Typically, we analyze patient or animal sera for pathogen profiling projects. However, our microarrays are also compatible with other samples such as plasma, CSF, or sputum. We're happy to discuss what's possible in a discovery call.
The exact amount depends on the experimental design, but for standard profiling projects, we typically work with 5–20 µg purified antibody or 10–40 µL serum or plasma.

Certainly! The flexibility and high capacity of our platform allows us to fully customize everything from content, to peptide length, to microarray layout. For broad screening, we also have a selection of pre-designed peptide microarrays that cover different pathogens which you can browse here.

As a matter of fact, we do. We offer a range of additional downstream assays (eg. ELISA, Luminex, functional T-cell assays), so depending on your project, we can provide additional contract research support beyond peptide microarray screening.

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