PEPperPRINT: PEPperCHIP® Human Epitome Microarray

PEPperCHIP® Peptide Microarrays - Data analysis

PEPperCHIP® Human Epitome Microarray

Discover unknown human antigens or cross-reactive antibodies by screening 23,163 human B-cell epitopes.

The PEPperCHIP^® Human Epitome Microarray covers 23,163 linear B-cell epitopes of the Immune Epitope Database. The peptide library contains selected epitopes of 3,209 different proteins from 591 different organisms. Moreover, the microarray contains HA, polio and c-Myc positive control peptides.

The PEPperCHIP^® Human Epitome Microarray can be used to investigate links between autoimmune and infectious diseases. The microarray can be also used for epitope mapping, serum screening, biomarker discovery and cross-reactivity analysis of therapeutic and diagnostic antibodies.

Due to the discovery microarray format and the resulting large data sets, PEPperCHIP^® Human Epitome Microarrays are exclusively provided in combination with our PEPperMAP^® Services.

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Fig.1. Epitope-wide screening with the PEPperCHIP® Human Epitome Microarray. Selected epitopes of 3,209 different proteins from 591 different organisms are converted into overlapping peptides and printed onto glass slides. Patient or animal serum is incubated on the microarray and antibodies present in the sample bind their corresponding epitopes on the microarray surface. The resulting response profiles can be The resulting response profile may be compared across different samples to monitor B-cell responses over time, or to determine immunodominant epitopes that may be further validated as potential disease-specific biomarkers for IVD development.

The PEPperCHIP^® Human Epitome Microarray enables the high throughput screening of serum and plasma antibody responses against all linear human B-cell epitopes of the Immune Epitope Database: This corresponds to a 29,128-peptide ELISA in a single assay with less than 100 µL sample required.

The PEPperCHIP^® Human Epitome Microarray can be used for the following applications

•	Epitome-wide antibody screening
•	Differentiation between IgG and IgM or IgA response profiles
•	High throughput serum biomarker discovery
•	Identification of prognostic epitopes
•	Cross-reactivity analysis of mono- and polyclonal antibodies
•	Patient stratification
•	Investigation of links between autoimmune and infectious diseases
•	Cross-reactivity analysis of therapeutic and diagnostic antibodies

See also

•	Application Note: Antibody Cross-Reactivity Profiling of a Human Monoclonal Antibody with the PEPperCHIP^® Human Epitome Microarray
•	Poster: High Resolution Epitope Mapping and Antibody Cross-Reactivity Analysis
•	Poster: High-Density Peptide Microarrays for Serum Biomarker Discovery

Microarray information

•	Microarray content: Sorted by disease states, the microarray covers B-cell epitopes selected from the Immune Epitope Database of the following indications: - 8,504 epitopes of infectious diseases - 3,808 epitopes of autoimmune diseases including 301 citrullinated peptides - 3,451 epitopes of allergens - 64 epitopes of transparent diseases - 199 cancer epitopes - 995 epitopes of other diseases - 1,481 epitopes of healthy controls - 4,661 epitopes of the most common vaccines
•	Database epitope lengths: 5 aa - 51 aa
•	Microarray epitope lengths: 5 to 17 aa depending on the epitope length; longer epitopes were translated into overlapping 17 aa peptides
•	Number of peptides / spots: 29,128 / 58,256 (peptides printed in duplicate)
•	Positive control: HA (YPYDVPDYAG), polio (KEVPALTAVETGAT) and c-Myc (EQKLISEEDL) control peptides (261, 257 and 257 spots each control)
•	Size and format: Discovery Format (10.5 cm x 11 cm) containing 1 array copy per chip
•	Accessories: only available in combination with our PEPperMAP^® Services

Sample information

•	Can be assayed with at least 100 µL serum/plasma or 100 µg/mL purified antibody.

Estimated delivery time

•	6-8 weeks when requested with PEPperMAP^® Services.

Documentation

•	PEPperCHIP^® Human Epitome Microarray Material Data Sheet [download pdf]
•	PEPperCHIP^® Human Epitome Microarray Peptide Map [download xlsx]

Learn how to perform the assay

•	PEPperCHIP^® Immunoassay Protocol [download pdf] [watch video]
•	PEPperCHIP^® Immunoassay Quickstart Guide [download pdf]

Steps	Materials and equipment	We recommend
Immunoassay	Incubation tray	PEPperCHIP^® Incubation Tray*
	Orbital shaker	-
	Blocking reagents	BSA, or Rockland Blocking Buffer*
	Control antibodies	PEPperCHIP^® Control Antibodies
	Buffers	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
Data analysis	Spreadsheet software	-

*used in-house by PEPperPRINT

274. Potential HIV vaccine gp41 epitope targeting antibodies identify peptides with similarity to proposed Kawasaki disease related peptide, suggesting non-specific mimotope targeting of acidic amino acid enriched regions. Hakimuddin, Sojar; Baron, Sarah; Hicar, Mark D. Open Forum Infectious Diseases. (2023 November). [doi.org/10.1093/ofid/ofad500.346]