• PEPperCHIP® Custom Peptide Microarrays



    PEPperCHIP® Custom Peptide Microarrays

    Quality microarrays uniquely created for your research 


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Your own personalized research tool

Fully customizable, infinitely scalable, quality-certified peptide microarrays

From single antigens to whole virus proteomes on a chip, PEPperCHIP® Custom Peptide Microarrays can be fully tailored to your scientific needs, whether you are looking to analyze antibodies, sera, or even full proteins.

Created with our award-winning PEPperCHIP® Platform Technology under ISO 9001 certifed quality control, each PEPperCHIP® Custom Peptide Microarray can be made with either linear or cyclic constrained peptides, as well as adapted to multiple chip formats to accomodate different experimental designs. Analyze several samples at once or screen against different antigens in one assay.

  •  PEPperCHIP® Custom Peptide Microarrays - Microarray formats
  •  PEPperCHIP® Custom Peptide Microarrays - Microarray formats

Advantages of high resolution PEPperCHIP® Peptide Microarrays

A new way to explore protein targets

Extensive libraries with maximally overlapping peptides for high-resolution analysis

Identify and characterize epitopes, compare antibody response profiles, or even investigate protein-protein interactions, right down to the last binding amino acid. Transform any protein target into highly-overlapping peptide libraries that can easily be analyzed using a fluorescence-based immunoassay. 

From high-throughput screening for antigen discovery, down to amino acid substitution scans to identify conserved and variable binding residues, get highly resolved epitope data from your samples.

Choose how you get your data

From DIY to contract research solutions, receive full scientific support

With every PEPperCHIP® Custom Peptide Microarray you order, the choice is yours: take full control and perform all microarray experiments at your own facility, or send us your samples and let us do the work for you. Get comprehensive support from our specialists no matter which option you choose.

Unsure about which solution is best suited for you? Get in touch with us for a free project assessment. 



DIY solution

with PEPperMAP® Service

Project consultationfreefree
Samples for analysisprocessed at your facilityshipped to PEPperPRINT
Immunoassayoptional add-on:
Data acquisitionrequires microarray scannerincluded
Data analysisoptional add-on:
MAPIX Analyzer software
Full scientific report-included
Dedicated customer supportincludedincluded
 Build your own kitChoose a service

Get your PEPperCHIP® Custom Peptide Microarray in 3 easy steps

Step 1

Send us your sequence

If you already know which proteins or antigens you would like to screen, simply enter the sequence information and peptide specifications using our online form below. 

Unsure of your target? Let us know using the form below, and one of our specialists will get in touch to help design a chip for you.

Step 2

Design your peptide library

Based on your input, we will propose an initital microarray design, which we will optimize together with you upon personal consultation about your project.

The final design will include positive assay controls compatible to your biological samples and experimental aim.

Step 3

Print your custom microarray

After consultation, we will generate and email you a peptide map which details the peptide library layout for final approval.  

Once approved, production begins, and your PEPperCHIP® Custom Peptide Microarray will be ready for immunoassay in 4-5 weeks.

In order to provide the best configured PEPperCHIP® Custom Peptide Microarray for your project, it helps us to learn about your scientific objectives. Consider including some of these additional details when sending us a quote request, either through our website, or personally through our team:

Nature and number of your samples: This information helps us select which positive control peptides to include on your chip, and which micorarray format would best accomodate your samples.   

Peptide characteristics: We routinely print maximally overlapping peptides (shift of 1 aa per peptide) to ensure analysis on a single amino acid level. However, the degree of overlap can be adjusted (shift 2 to 6) to include more peptides on the array or array copies to the overall chip design. If providing a list of peptides, those peptides with be directly considered for the peptide microarray design.

Non-natural amino acids: In addition to proteinogenic amino acids, we can also print additional monomers and include some post-translational modifications. A list of all printable monomers can be found here

 Standard formatDiscovery format
Microarray contentcan be designed with any amino acid sequence of your choicecan be designed with any amino acid sequence of your choice
Peptide lengths and overlapsLinear - typically 15aa peptides with peptide-peptide overlap of 14 (shift 1)
Cyclic constrained - typically 7, 10, and 13aa peptide with peptide-peptide overlaps of 6, 9, and 6aa respectively (shift 1).
Custom peptide lengths on request.
Linear - typically 15aa peptides with peptide-peptide overlap of 14 (shift 1)
Cyclic constrained - typically 7, 10, and 13aa peptide with peptide-peptide overlaps of 6, 9, and 6aa respectively (shift 1).
Custom peptide lengths on request.
Number of peptides/spotsup to 11,288 or 5,644 in duplicatesup to 75,460 or 37,730 in duplicates
Positive controlstypically HA (YPYDVPDYAG) and polio (KEVPALTAVETGAT) control peptides; other control peptides on requesttypically HA (YPYDVPDYAG) and polio (KEVPALTAVETGAT) control peptides; other control peptides on request
Size and format75.4 mm x 25.0 mm x 1.0 mm (3" x 1")10.5 cm x 11 cm (4.13" x 4.33")
Accessoriescompatible with PEPperCHIP® Incubation Trays in different formats only available in combination with PEPperMAP® Services
Sample informationat least 20 µL serum/plasma or 10-20 µg/mL purified antibodyat least 70 µL serum/plasma or 70-100 µg/mL purified antibody
Estimated delivery time4-5 weeks for chip and optional add-on accessories
6-8 weeks when requested with PEPperMAP® Services
4-5 weeks for chip and optional add-on accessories
6-8 weeks when requested with PEPperMAP® Services

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



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

How stable are the printed arrays? How long can they be stored?
PEPperCHIP® Peptide Microarrays should be stored at 4°C in the dark to ensure a long shelf life. If handled with care, chips are stable for months. If possible, please store them under inert gas atmosphere.

Can arrays be used several times?
In theory the arrays can be stripped. However, the stripping efficiency always depends on the nature of the samples and the assays. It may not work in all cases, and the chips may also degrade to some extent. Stripping efficiency has to be checked by microarray scanning, and even then you likely will not know if you removed all primary antibodies, or only the secondary antibody. Since we can print multiple array copies per chip (number of copies depends on the size of the array) we recommend using a new array for each experiment.

How is the accuracy of the (printed) peptide sequence checked?
Due to the high number of different peptides (up to 70,000 in a discovery format) and the picomolar amount, it is technically impossible to analyze all synthesized peptides in HPLC. Nevertheless, we perform numerous quality tests during production setup: We routinely run double coupling steps to get as close as possible to quantitative coupling yields. After coupling, non-reacted amino groups are capped to avoid the formation of peptides with incomplete sequences. According to HPLC analysis and mass spectrometry with reference peptides, side reactions like aspartimide and β-lactam formation or racemization can be excluded.

Ready to discuss your project?

Talk to one of our specialists to get started

Get in touch »Request a quote »

Get started with your own PEPperCHIP® Custom Peptide Microarray

Custom Peptide Microarray Request Form

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For multiple microarray requests, we recommend using our general PEPperCHIP® Peptide Microarray request form.
For service requests with PEPperCHIP® Custom Peptide Microarrays, we recommend using any of our PEPperMAP® Service request forms for additional options.

Your PEPperCHIP® Peptide Microarray details

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Your sample analysis

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