Epitope Mapping
Identify linear or conformational epitopes on the amino acid level
On a target protein, binding sites may be localized within continuous peptide sequences and interact as linear epitopes, or may stretch across different points within the sequence and interact as conformational epitopes. PEPperPRINT's unique PEPperCHIP® Platform Technology supports synthesis of linear and cyclic constrained peptides which mimic linear and looped epitope structures, enabling microarray-based mapping of linear and conformational epitopes.
Linear epitope mapping is the the standard epitope mapping format based on a single peptide length and the maximum peptide overlap for high resolution epitope data, and is often the recommended solution for monoclonal antibodies. Conformational epitope mapping is based on an antigen translated into 7, 10 and 13 amino acids cyclic constrained peptides with maximum peptide overlaps of 6, 9 and 12 amino acids. Different peptide lengths are applied to mimic different loop sized and hence epitope conformations.
Unsure whether your epitopes might be linear or conformational? Talk to one of our experts for a free project assessment.
Linear Mapping | Conformational Mapping | |
|---|---|---|
| Microarray content | Single to multiple antigens converted into overlapping peptides | Single to multiple antigens converted into overlapping peptides |
| Peptide length | 15 amino acids by default (adjustable) | 7, 10 and 13 amino acids by default (adjustable) |
| Peptide overlap | 14 amino acids by default (adjustable) | 6, 9 and 12 amino acids by default (adjustable) |
| Technical replicates | Peptide double spots by default (adjustable) | Peptide double spots by default (adjustable) |
| Built-in control peptides | HA (YPYDVPDYAG) epitopes by default | HA (YPYDVPDYAG) epitopes by default |
| Input data | Peptide list, UniProt ID, or protein sequence(s) in the FASTA format | Peptide list, UniProt ID, or protein sequence(s) in the FASTA format |
| Sample material | at least 20 µg per sample | at least 70 µg per sample |
Antigen Discovery and Cross-reactivity Analysis
Identify antigenic targets or analyze antibody specificity
Antibodies are essential tools for therapeutic, diagnostic and research purposes. However, antibodies are often poorly characterized in terms of specificity and cross-reactivity. PEPperPRINT offers multiple solutions for target discovery and profiling antibody cross-reactivities against human proteins, human B-cell epitopes, or other disease- or pathogen- specific antigens:
- Protein-level screening with the HuProtTM Human Proteome Microarray (currently only available for customers based in Europe)
- Antigen screening with the PEPperCHIP® Human Epitome Microarray
- Epitope-level screening with PEPperCHIP® Peptide Microarrays
HuProtTM Proteome Microarray | PEPperCHIP® Human Epitome Microarray | PEPperCHIP® Peptide Microarrays | |
|---|---|---|---|
| Microarray content | over 21,000 human proteins | 29,128 peptides covering all linear B-cell epitopes of the Immune Epitope Database | Multiple antigens translated into up to 35,000 overlapping peptides in duplicates |
| Species | Human | Human, animal, and various pathogens | Human, animal, any pathogen, or random peptides |
| Peptide length | - | 5 to 17 amino acids depending on epitope length; longer epitopes translated into overlapping peptides | typically 15 amino acids |
| Peptide overlap shift | - | shift +1 | typically shift +1 (adjustable) |
| Sample material | at least 10 µg per sample | at least 100 µg per sample | at least 20 µg per sample |
| Recommended applications | Antigen discovery or antibody cross-reactivity analysis | Antigen discovery or antibody cross-reactivity analysis | Antigen discovery |
Epitope Substitution Scan
Identify conserved and variable amino acid positions of any epitope
Epitope substitution scans cover the stepwise substitution of all amino acid positions of a given epitope or peptide with all 20 main amino acids and optionally additional non-natural amino acids. Validate binding specificity or optimize peptide leads by analyzing single amino acid substitution effects on binding affinity.
| Microarray content | Gradual exchange of all amino acid positions with all amino acids |
| Peptide length | Up to 20 amino acids |
| Motif length for scan | Up to 20 amino acids |
| Technical replicates | Peptide triple spots by default (adjustable) |
| Built-in control peptides | HA (YPYDVPDYAG) epitopes by default |
| Input data | Wild type epitope or sequence |
| Sample material | at least 20 µg per sample |
How to get started with your PEPperMAP® Service
Step 1
Tell us about your targets
If you already know which peptides, proteins or antigens you would like to screen, simply send us the sequence information via email, or through our request forms. This information will help us design a custom or select a pre-designed microarray for your project.
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
Select your service package
The comparison guide below outlines typical inclusions and available customizations for PEPperMAP® Antibody Services. Prices and turnaround times may vary depending on the number of samples, complexity of experimental setup, and the type of data analysis requested.
To get a quote, simply fill in the request form at the end of the page.
Step 3
Send us your samples
Our microarrays can be used to analyze peptides, antibodies or nanobodies, sera, or even full proteins. The amount and concentration of samples you would need to send us will depend on the experimental setup, which will also be covered in the project consultation.
For custom microarray projects, chips will include positive assay controls compatible to your biological samples and experimental aim.
PEPperMAP® Essential covers the basic service componets necessary to deliver raw sample analysis data. The following are included:
PEPperCHIP® Custom or Standard Peptide Microarrays | |
• | Your protein or peptide sequence/s as overlapping peptides, or any of our pre-designed PEPperCHIP® Standard Peptide Microarrays |
• | Peptides printed in duplicate per array copy |
• | Built-in postive controls: HA (YPYDVPDYAG), polio (KEVPALTAVETGAT), c-Myc (EQKLISEEDL) or custom peptides by request |
or, for discovery or cross-reactivity analyses projects,
HuProtTM Human Proteome Microarray v4.0 (available for customers within Europe) | |
• | Functional protein microarray |
• | Over 21,000 human proteins, isoform variants, and protein fragments |
Data Acquisition | |
• | All immunoassays with your samples or analytes |
• | Staining with control and secondary antibodies |
• | High-resolution scanning of processed micorarray and read-out data export |
Data Quantification and Formatting | |
• | Quantification of microarray data |
• | Data formatting in Excel |
• | Generation of data summaries and charts |
PEPperMAP® Standard includes everything int the Essential Package, along with some additional reporting features:
PEPperCHIP® Custom or Standard Peptide Microarrays | |
• | Your protein or peptide sequence/s as overlapping peptides, or any of our pre-designed PEPperCHIP® Standard Peptide Microarrays |
• | Peptides printed in duplicate per array copy |
• | Built-in postive controls: HA (YPYDVPDYAG), polio (KEVPALTAVETGAT), c-Myc (EQKLISEEDL) or custom peptides by request |
or, for discovery or cross-reactivity analyses projects,
HuProtTM Human Proteome Microarray v4.0 (available for customers within Europe) | |
• | Functional protein microarray |
• | Over 21,000 human proteins, isoform variants, and protein fragments |
Data Acquisition | |
• | All immunoassays with your samples or analytes |
• | Staining with control and secondary antibodies |
• | High-resolution scanning of processed micorarray and read-out data export |
Data Quantification and Formatting | |
• | Quantification of microarray data |
• | Data formatting in Excel |
• | Generation of data summaries and charts |
• | Epitope annotation(s) |
Data Reporting | |
• | Scientific reporting (includes materials and methods and experimental section) |
• | Data evaluation and discussion |
For projects with multiple samples or experimental conditions, additional services may be available based on applicability:
Bioinformatic analyses | |
• | Extensive statistical analyses including data normalization, data clustering or the generation of heat maps can be performed based on the scientific questions required by the project |
Affinity determination service | |
• | Kd/EC50 determination via fluorescence polarization assays |
Hit validation services | |
• | ELISA- or Luminex-based validation immunoassays |