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Cancer Immunology & Neoantigen Discovery

Discover tumor-specific antigens, profile anti-tumor antibody responses, and characterize therapeutic antibodies for precision cancer immunotherapy. Map B- or T-cell epitopes and identify treatment biomarkers for comprehensive immune profiling.
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What peptide microarrays enable

Profile anti-tumor immunity at epitope resolution

Cancer immunology spans discovery of tumor antigens, development of therapeutic antibodies, and identification of biomarkers predicting treatment response and resistance. Peptide microarrays connect these stages by enabling epitope-level profiling across both research and development workflows.

Table of Contents

Discover & profile tumor-specific immune responses

Map antibody responses to neoantigens and tumor-associated antigens to characterize anti-tumor immunity.

Screen neoantigens and tumor-associated antigens

Test patient sera against tumor-specific mutations and shared cancer antigens to identify which epitopes elicit antibody responses.

Profile immune responses before, during, and after treatment

Track antibody recognition patterns across treatment timelines to understand how immunotherapy shapes anti-tumor immunity.

Characterize individual immune repertoires

Map patient-specific antibody profiles to reveal why some individuals mount strong anti-tumor responses while others don't.

Develop & characterize cancer-targeting therapeutics

Validate therapeutic antibodies targeting tumor antigens for drug development.

Map epitopes to validate antibody specificity

Confirm therapeutic antibodies bind intended targets with high resolution epitope mapping before advancing to clinical development.

Differentiate from existing therapies

Show your antibody binds a distinct epitope versus approved drugs, supporting development of differentiated therapeutic candidates.

Guide ADC and bispecific antibody design

Characterize binding sites to inform antibody-drug conjugate development or design companion imaging agents that don't interfere with treatment.

Identify biomarkers for treatment response & resistance

Discover antibody signatures that predict immunotherapy outcomes or reveal resistance mechanisms.

Screen cohorts to find response-predictive patterns

Profile patient populations to identify antibody signatures correlating with checkpoint inhibitor response or disease progression.

Detect resistance pathway activation

Identify antibodies against compensatory pathways (e.g., alternative angiogenesis factors) that mediate treatment resistance.

Support patient stratification research

Map immune signatures that may inform precision oncology approaches for selecting patients most likely to benefit from specific therapies.

Research questions answered

Customer breakthroughs in cancer immunology

Researchers use peptide microarrays to uncover mechanisms of anti-tumor immunity, develop novel therapeutics, and identify biomarkers predicting treatment outcomes. Here’s how epitope-level profiling advances cancer immunology research.

Breast cancer
Which tumor antigens elicit immune responses during immunotherapy?
Custom arrays screening tumor-specific mutations plus self-antigens in triple-negative breast cancer patients undergoing checkpoint inhibitor therapy revealed strong anti-EPS8 (self-antigen) antibodies in a patient with complete response, showing both neoantigen and self-antigen immunity contribute to treatment success.
Routh ED et al., 2023 ↗​
Glioblastoma
Can I find non-invasive biomarkers for early cancer detection?
Screening sera against tumor-associated antigens identified IgM signature patterns distinguishing glioblastoma patients from controls, revealing potential non-invasive diagnostic biomarkers for brain tumors detectable before imaging abnormalities.
Ferdinandov D et al., 2023 ↗​
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 ↗​
CD30+ Cancers
Does my therapeutic antibody bind a unique epitope versus existing drugs?
Epitope mapping of anti-CD30 bispecific antibody showed binding to a distinct region from brentuximab vedotin, confirming unique mechanism of action and supporting development as a differentiated cancer therapeutic for CD30+ malignancies.
Faber ML et al., 2023 ↗​
How it works

From antibody profiling to T-cell epitope validation

Cancer immunity involves both antibody responses (B-cell immunity) and cellular responses (T-cell immunity). Peptide microarrays enable profiling of both: screen patient sera to map antibody recognition, test recombinant HLA molecules to identify T-cell epitopes, and validate candidates with functional T-cell assays for comprehensive immune characterization.
Peptide microarrays serve as the discovery platform for both B-cell and T-cell epitopes. Start with antibody profiling to identify tumor antigens, then validate T-cell epitopes using HLA-binding assays and functional T-cell readouts.

Need help designing your study? Let’s discuss.

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PROJECT WORKFLOW

What an immune profiling project for cancer studies looks like

Whether you’re investigating tumor immunology or developing cancer therapies, using a peptide microarray approach is straightforward. 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 target sequence/s. We're happy to sign an NDA in the case of proprietary sequence information.
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 target sequence/s. We're happy to sign an NDA in the case of proprietary sequence information. 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

Dive deeper

Looking to validate T-cell epitopes?

Tumor immunology is complex. For cancer vaccines and immunotherapies where cellular immunity matters, T-cell profiling delivers a complete picture of adaptive immune responses.

Explore T-cell services
Related applications

Beyond immuno-oncology

Tumor immunity profiling connects to multiple research contexts. Here's where cancer immunology research often go next:
Antibody Research & Epitope Mapping
Map binding sites, detect cross-reactivity, and identify critical residues for therapeutic antibody characterization.
Explore application →
Vaccine & Therapeutic Immunogenicity Profiling
Profile immune responses for vaccine optimization, anti-drug antibody detection, and immunotherapy development across preclinical to clinical stages.
Explore application →

Profile anti-tumor immunity at epitope resolution

Whether you're discovering neoantigens, characterizing therapeutic antibodies, or identifying treatment biomarkers, peptide microarrays deliver the detailed immune landscape needed to understand why some patients respond to immunotherapy while others don't. Not sure which approach fits your cancer research? Let's talk through it.
Explore your study design
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Frequently Asked Questions

Before you get started

How do peptide microarrays fit into cancer immunology research?
Cancer immunology research traditionally focuses on T-cell responses, but antibody-mediated immunity also plays important roles in tumor recognition, immune surveillance, and treatment response. Peptide microarrays uniquely profile B-cell immunity by mapping which tumor antigens patient antibodies recognize. Arrays complement T-cell assays by revealing the humoral side of anti-tumor immunity, which is useful for neoantigen discovery, biomarker identification, and understanding why antibody responses correlate with immunotherapy outcomes in some patients.
We use a peptide scanning approach based on a fluorescence-based immunoassay to detect and characterize sequence-specific interactions. In the context of immuno-oncology, often this means analyzing responses against either neo or tumor-associated antigens, or therapeutic targets. We convert these sequences into a library of overlapping peptides, incubate it with patient sera, stain it with a secondary antibody, and identify the epitope signatures by quantifying fluorescent signals of each peptide on the array.
Neoantigens are patient-specific antigens arising from tumor mutations unique to each patient's cancer. Peptide microarrays can screen predicted neoantigens from tumor sequencing to validate which ones actually elicit immune responses. Tumor-associated antigens (TAAs) are proteins overexpressed or aberrantly expressed in tumors but also present in normal tissues (like HER2, MAGE family, or cancer-testis antigens). Arrays can screen both: patient-specific neoantigens for personalized approaches, or shared TAAs to understand common immune recognition patterns across cancer types.

Yes. While peptide microarrays traditionally profile antibody responses, we also offer HLA-binding assays using recombinant HLA-II to identify peptides that bind MHC molecules for T-cell presentation. Candidate T-cell epitopes can be validated with functional assays (e.g., ELISpot, T-cell killing assays) through our service labs. This integrated workflow lets you characterize both B-cell and T-cell immunity in a single study. Contact us to discuss your specific research needs and which assays best fit your questions.

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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