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Autoimmune & Neurodegenerative Diseases

Discover disease-associated autoantigens, map autoantibody epitopes, and profile patient populations to understand complex immune-mediated conditions. From rheumatoid arthritis to Alzheimer's, identify biomarkers and characterize modification-specific responses.
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What peptide microarrays enable

Decode disease-associated antibody responses

Many autoimmune and neurodegenerative diseases involve complex antibody responses against self-proteins. Peptide microarrays reveal exactly where antibodies bind, enabling researchers to discover novel autoantigens, identify disease-associated antibody signatures, and map modification-dependent epitopes involved in immune recognition.

Table of Contents

Discover disease-associated autoantigens

Screen patient sera against comprehensive antigen libraries to identify novel disease-associated antibodies.

Screen broad antigen libraries for unbiased discovery

Test patient sera against comprehensive protein or peptide libraries to identify candidate autoantigens linked to disease.

Validate hits across patient cohorts

Test candidate autoantigens against focused custom peptide libraries to distinguish disease-specific signals from individual variation.

Reveal unexpected immune targets

Identify antibody responses against proteins not previously associated with autoimmune or neurodegenerative disease mechanisms.

Identify antibody signatures for early detection studies

Profile antibody patterns across patient cohorts to uncover immune signatures associated with disease risk, onset, subtypes, or outcomes.

Identify early biomarker candidates before symptoms emerge

Screen patient cohorts to find autoantibody patterns that appear before clinical diagnosis, enabling earlier detection research.

Distinguish disease subtypes and severity

Identify epitope-specific antibody responses that may distinguish patients from healthy controls or different disease stages.

Validate immune signatures across populations

Confirm candidate antibody signatures across larger cohorts to support biomarker discovery and translational research.

Map epitopes & post-translational modification dependencies

Characterize exactly where autoantibodies bind and whether recognition depends on site-specific modifications.

Identify epitopes at single amino acid resolution

Screen overlapping peptides to pinpoint exact binding regions and define critical residues for antibody recognition.

Test modification-specific autoreactivity

Profile responses to citrullinated, phosphorylated, or otherwise modified peptides to reveal PTM-dependent binding patterns.

Compare modified versus unmodified peptide recognition

Direct side-by-side testing shows whether autoantibodies require specific modifications like citrullination (RA) or phosphorylation (SLE).

Research questions answered

Customer breakthroughs in autoimmune & neurodegenerative research

Which antigens trigger immune recognition, which epitopes drive the response, and how do these patterns correlate with disease? Peptide microarrays help researchers answer those questions directly.

Biomarker discovery
Can autoantibody signatures predict disease risk?
Screening cardiac ion channel epitopes revealed anti-TRPV2 autoantibodies in 84.6% of sudden infant death syndrome (SIDS) cases versus 25% in healthy controls, guiding follow-up mechanistic studies and establishing a potential biomarker for identifying at-risk infants before tragedy strikes.
Maguy A et al., 2025 ↗​
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 ↗​
Neurodegeneration biomarker
Are there sex-specific immune markers for Alzheimer's risk?
Peptide microarray profiling of 3,359 epitopes including viral and autoimmune antigens revealed reduced anti-DG#29 IgG (targeting EBV EBNA1) in women with Alzheimer's versus controls. Low antibody levels plus recent EBV reactivation increased AD odds 8.7-fold, but only in women.
Sim KY et al., 2024 ↗​
How it works

From autoantigen discovery to epitope characterization

Autoimmune studies often begin with a simple question: what exactly is the immune system reacting to? Microarray-based screening lets you move from broad antigen discovery to detailed epitope characterization in a single experimental pipeline.
How it works

From autoantigen discovery to epitope characterization

Autoimmune studies often begin with a simple question: what exactly is the immune system reacting to? Microarray-based screening lets you move from broad antigen discovery to detailed epitope characterization in a single experimental pipeline.

Need help designing your study? Let’s discuss what’s possible.

Start the conversation
PROJECT WORKFLOW

What an autoimmune profiling project looks like

Autoantigen 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.
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 epitope mapping

Antibody characterization rarely ends with the epitope. Here's what researchers typically explore 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 →

Cancer Immunology & Neoantigen Discovery

Characterize antibodies targeting tumor-associated antigens and validate binding specificity against clinical candidates.
Explore application →

Infectious Disease & Pathogen Profiling

Profile immune responses to viral and bacterial antigens for vaccine development, seroprevalence studies, and pathogen surveillance.
Explore application →

Searching for elusive autoantibody targets or early biomarkers?

Whether you're discovering novel autoantigens, mapping epitopes, or profiling patient cohorts, peptide and protein microarrays deliver the detailed immune landscape needed to understand complex autoimmune and neurodegenerative diseases.Not sure which approach fits your cancer research? Let's talk through it.
Start the conversation
Request a quote
Frequently Asked Questions

Before you get started

How do you profile autoantibody responses?
Put simply, we perform epitope mapping on antibodies present in serum or other complex biological samples. For this, we use a peptide scanning approach using a fluorescence-based immunoassay. First, we convert your target antigens or proteins into overlapping peptides on a chip (we can also generate random peptide sequences to screen for binding motifs if targets are unknown). Then, we incubate the chip with your sample, stain it with a secondary antibody, and identify the 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.
We recommend starting with protein microarrays (HuProt™) if you don't know which proteins your patient autoantibodies target. This enables unbiased discovery across 21,000+ human proteins. Start with peptide microarrays if you already know your target antigens and want to map exact epitopes or test PTM dependencies. Use both for comprehensive characterization: protein arrays for discovery, peptide arrays for epitope-level detail.

We can generate peptides that are citrullinated, methylated, phosphorylated. D-amino acid variants can be synthesized as well. You can find a complete list of available amino acids and monomers here.

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.

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