PEPperCHIP® Cancer Neoepitope Microarray

Translate cancer point mutations into personalized peptide microarrays. Profile B-cell neoepitopes and tumor-associated antigen responses in a single assay.

The PEPperCHIP® Cancer Neoepitope Microarrays is a customized peptide microarray covering up to 5,500 peptides in duplicates for the personalized analysis of anti-tumor antibody responses. The microarray can be designed using up to 2,750 wild type vs. mutant peptide pairs or using a combination of genomic sequencing derived protein and /or tumor-associated antigens as highly overlapping peptides. The degree of peptide-peptide overlap (e.g. shift 1 to 3) can be selected. Moreover, the microarray contains HA, polio and c-Myc positive control peptides.

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Each tumor exhibits an individual cancer mutation profile with shared and patient unique mutations. The resulting neoantigens can elicit strong immune responses with detectable antibody levels in patient sera.

The fingerprint analysis of antibody profiles to neoepitopes could precisely distinguish between immunogenic and non-immunogenic mutations, a prerequisite for high-precision cancer immunotherapy and cancer vaccine development. Antibody responses to neoepitopes could be compared in treatment responders and non-responders to search for predictive biomarkers.

Furthermore, neoepitope response profiles could be a source to predict side effects to therapy. 

The PEPperCHIP® Cancer Neoepitope Microarray can be used for the following applications


Validate therapeutic antibodies against tumor associated antigens


Target Discovery: Identify immunogenic epitopes for immunotherapy


Develop personalized cancer vaccines


Monitor patient-specific anti-tumor antibody responses


Discover prognostic cancer neoepitopes


What our customers say

"We have rigorously tested the reproducibility, sensitivity, and specificity of peptide microarrays provided by the PEPperPRINT using biological samples and have published two papers. […] We found this platform to be extremely useful for our studies. These dedicated efforts are testament to the standard of excellence maintained by PEPperPRINT’s scientific staff, for continued improvement and innovation of peptide microarray technology." 

Prof. David Han, UConn Health

Microarray information


Microarray content: Custom cancer neoepitope microarray corresponding to 2750 wild type/mutant peptide pairs


Peptide length and overlap: 3 aa to 15 aa depending on the epitope length


Number of peptides / spots: 5,500 / 11,000 (peptides printed in duplicate)


Positive control: HA (YPYDVPDYAG), polio (KEVPALTAVETGAT) and c-Myc (EQKLISEEDL) control peptides 


Size and format: 3'' x 1'', 75.4 mm x 25.0 mm x 1.0 mm, containing 1 array copy per chip


Accessories: compatible with 3/1 well PEPperCHIP® Incubation Tray


Sample information


Can be assayed with at least 20 µL serum/plasma or 10-20 µg/mL purified antibody.


Estimated delivery time


1-4 weeks for chip and optional add-on accessories


6-8 weeks when requested with PEPperMAP® Services.




PEPperCHIP® Cancer Neoepitope Microarray product flyer [download pdf]


Learn how to perform the assay­­­


PEPperCHIP® Immunoassay Protocol [download pdf] [watch video]


PEPperCHIP® Immunoassay Quickstart Guide [download pdf]



Materials and equipment

We recommend


Incubation tray

PEPperCHIP® Incubation Tray*

Orbital shaker


Blocking reagents

BSA, or Rockland Blocking Buffer*

Control antibodies

PEPperCHIP® Control Antibodies


PBS, Tween 20

Labelled secondary antibodies

Rockland secondary antibodies*

Data acquisition

Microarray scanner

Innopsys InnoScan® 710/710-IR*
LI-COR Odyssey® scanners*

See a list of compatible scanners

Data analysis

Fluorescence spot intensity quantification software

MAPIX Analyzer by Innopsys

Spreadsheet software


*used in-house by PEPperPRINT



Discovery of Putative Breast Cancer Antigens Using an Integrative Platform of Genomics-Driven Immunoproteomics.
Veneta Qendro, Deborah H. Lundgren, Samuel Palczewski, Poornima Hegde, Christina Stevenson, Laurie Perpetua, Ardian Latifi, Jesse Merriman, Grace Bugos, and David K. Han. PROTEOMICS 17, no. 15–16 (August 2017): 1600318. [

Integrative Proteomics, Genomics, and Translational Immunology Approaches Reveal Mutated Forms of Proteolipid Protein 1 (PLP1) and Mutant-Specific Immune Response in Multiple Sclerosis.
Veneta Qendro, Grace A. Bugos, Debbie H. Lundgren, John Glynn, May H. Han, and David K. Han. PROTEOMICS 17, no. 6 (March 2017): 1600322. []

Genomics-Driven Immunoproteomics: An Integrative Platform to Uncover Important Biomarkers for Human Diseases.
Raghavendra Giri, Veneta Qendro, Pooja Rani, Carren Jepchumba, Grace Bugos, Volker Stadler, and David K. Han. In Immunoproteomics, edited by Kelly M. Fulton and Susan M. Twine, 2024:327–32. New York, NY: Springer New York, 2019. []

PEPperCHIP® Cancer Neoepitope Microarray

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<s>For off-the-shelf products, see Standard chips and accessories checklist.xlsx for the product description that goes in this section.</s>

<s>475.00 EUR</s>

Excl. tax and shipping costs.

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