High Resolution Epitope Mapping

PEPperCHIP® Peptide Microarrays enable the high resolution epitope mapping of antibodies and sera by translating one or more antigens into overlapping peptides. Incubation of the resulting peptide microarray with an antibody or serum sample as well as suited secondary antibodies gives rise to spot patterns that correlate with the epitope of the given sample.


Due to the very high spot density and the widely unlimited peptide content flexibility, PEPperCHIP® Peptide Microarrays are the ideal and most economic solution to identify antibody and serum epitopes in the highest resolution possible. 


High resolution epitope mappings can be based on e.g. a single antigen using PEPperCHIP® Custom Peptide Microarrays with standard dimensions or on hundreds of proteins at once using large scale PEPperCHIP® Discovery Microarrays.

 

 

Specifications of Type 1 Epitope Mapping

The Type 1 Epitope Mapping is the standard epitope mapping format based on a single peptide length and the maximum peptide overlap for high resolution epitope data. The Type 1 Epitope Mapping is the recommended solution for monoclonal antibodies and serum samples.

Type 1 Epitope Mapping

PEPperMAP® Type 1 Epitope Mapping of a monoclonal antibody against an antigen translated into 15 aa peptides with 14 aa peptide overlap. The microarray scan (left) as well as the intensity plot (right) reveal a stretch of adjacent peptides with a consensus motif that represents the epitope of the antibody. Stained HA (red) and Flag (green) control peptides frame the antigen-derived peptides.

 

   Microarray Content:    Single to multiple antigens translated into overlapping peptides
   Peptide Length:    15 amino acids by default (adjustable)
   Peptide Overlap:    14 amino acids by default (adjustable)
   Peptide Repeats:    Peptide double spots by default (adjustable)
   Control Peptides:    HA (YPYDVPDYAG) and Flag (DYKDDDDKAS) tags by default
   Microarray Example:    A protein sequence of 400 amino acids will be translated into 2 x 400 different peptides

 

 

Specifications of Type 2 Epitope Mapping

The Type 2 Epitope Mapping is based on antigen-derived peptides with three different lengths (usually 10, 12 and 15 aa) with maximum peptide overlap for high resolution epitope data. The Type 2 Epitope Mapping allows the itemization of possibly overlapping adjacent epitopes in polyclonal samples, or the analysis of any effect of peptide length on antibody binding. The Type 2 Epitope Mapping covers the threefold amount of data points compared to a Type 1 Epitope Mapping.

Type 2 Epitope Mapping

PEPperMAP® Type 2 Epitope Mapping of a polyclonal antibody against an antigen translated into 10, 12 and 15 aa peptides with 9, 11 and 14 aa peptide overlap. The microarray scan (left) as well as the intensity plot (right) of the 15 aa peptides shows an apparent single epitope stretch which can be separated in two adjacent epitopes with the 10 and 12 aa peptides. Stained HA (red) and Flag (green) control peptides frame the antigen-derived peptides.

 

   Microarray Content:    Single to multiple antigens translated into overlapping peptides
   Peptide Length:    10, 12 and 15 amino acids by default (adjustable)
   Peptide Overlap:    9, 11 and 14 amino acids by default (adjustable)
   Peptide Repeats:    Peptide double spots by default (adjustable)
   Control Peptides:    HA (YPYDVPDYAG) and Flag (DYKDDDDKAS) tags by default
   Microarray Example:    A protein sequence of 400 amino acids will be translated into 2 x 1,200 different peptides


 

Input Data & Sample Material

  • Protein sequence(s) in the FASTA format or with UniProt ID
  • 10-20 µl serum or 10-20 µg purified antibody



Analysis

PEPperCHIP® Peptide Microarray analysis is straightforward and can be performed in your own lab or covered by a PEPperMAP® Service. PEPperMAP® Type 1 and Type 2 Epitope Mappings are based on cost effective flat-rate fees. Information about lab requirements for PEPperCHIP® Peptide Microarray analysis can be found here.

 

 

Further Information

 

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