Antibody profiling
Get epitope-level fingerprint analysis of antibody responses
Complex biological samples such as sera or plasma contain a diverse mix of antibodies that together present a snapshot of a subject's immunological state. PEPperCHIP® Peptide Microarrays are an ideal tool for identifying and characterizing epitope-level antibody reactivities against multiple antigens at once.
We combine high-resolution peptide microarray data with years of expertise working with immunologically complex samples to deliver in-depth antibody fingerprint analyses. 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 epitope signatures in complex samples such as sera, plasma, or other similar analytes.
What are some use-cases of antibody profiling?
Immune monitoring in drug or vaccine development
Immune monitoring allows the fingerprint analysis of antibody responses upon immunization, vaccination or administration of a biopharmaceutical drug. In contrast to an ELISA, which only states whether antibodies against the antigen are present or not, antibody profiling with PEPperCHIP® Peptide Microarrays allows for the characterization of humoral immune response into high and low immunogenic epitopes.
B-cell repertoires in allergy or autoimmune disease
Some antibody reactivities can either lead to allergies due to an overreaction to otherwise harmless antigens, or autoimmune diseases due to self-directed antibodies. Fingerprint analyses with PEPperCHIP® Peptide Microarrays can reveal these antibody signatures down to the amino acid level, and which can shed some insight on the baseline cause of these over-reactive antibodies.
Application note: Human Autoantibody Screening with the PEPperCHIP® Autoimmune Epitope Microarray 2.0
Clinical trial monitoring and anti-drug antibody analysis
Whether you want to check patient sera for antibodies against gene therapy vectors or for anti-drug antibodies, PEPperCHIP® Peptide Microarrays allow for an in-depth characterization of the current immunological status of a patient before administering a drug or other therapeutic against selected antigens. Resulting antibody profiles can provide valuable information which can guide patient stratification or hold predictive indicators for therapeutic outcome.
Antibody response during infection
A subject's antibody composition and its corresponding epitope landscape can reveal previous exposure to infectious agents or the development of immune responses to disease. Antibody profiling with PEPperCHIP® Peptide Microarrays can reveal immunogenic regions in a pathogens proteome, antibody cross-reactivity between different pathogens, or the developemnt of autoantibodies after infections.
Application note: Fine Mapping of the Hepatitis E Virus Immune Response Using High Resolution Linear and Conformational Peptide Microarrays
Serum biomarker discovery
Serologically screen thousands of peptides and hundreds of antigens at once
The identification of early biomarkers for severe diseases by noninvasive methods is highly relevant, but demanding. PEPperPRINT's high-content peptide microarrays provide a very efficient tool for antibody biomarker discovery from sera. Screen entire pathogen proteomes for epitope markers for disease or immunity, identify immunogenic hotspots, or characterize changes in antibody response patterns. The flexibility of the PEPperCHIP® platform allows the step-wise screening from up to 35,000 peptides for hit discovery down to handful peptides for hit validation.
PEPperCHIP® Discovery format | PEPperCHIP® Standard format | |
|---|---|---|
| Microarray content | Single to multiple antigens translated into overlapping peptides | Single to multiple antigens translated into overlapping peptides |
| Pre-designed content available | PEPperCHIP® Human Epitome Microarray, or random peptides for immunosignature discovery | PEPperCHIP® Standard Peptide Microarrays (over 40 different microarrays available) |
| Number of peptides | Up to 35,000 (in duplicate) | Up to 5,500 (in duplicate) |
| Available peptide conformations | Linear and cyclic constrained peptides | Linear and cyclic constrained peptide |
| Built-in control peptides | HA (YPYDVPDYAG) epitopes by default | HA (YPYDVPDYAG) epitopes by default |
| Input data (for custom content) | Peptide list, Database ID, or protein sequence(s) in the FASTA format | Peptide list, Database ID, or protein sequence(s) in the FASTA format |
| Sample material | At least 70 µL per sample | At least 20 µL 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® Serum+ 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, when selected,
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. It is our recommended cost-effective solution for projects with multiple samples or sample groups.
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, when selected,
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 annotations |
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:
Dual-isotype mapping | |
• | Screening and analysis of your sample/s with an additional antibody isotype on the same microarray. |
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 |
Binding motif analyses | |
• | Multiple Em for Motif Elicitation (MEME) analyisis - discovery of common motifs, essential and conserved amino acid positions in the top peptide hits. |
• | Find Individual Motif Occurences (FIMO) analysis - database blasting of MEME selected motifs to identify protein candidates for cross-reactions. |
Affinity determination service | |
• | Kd/EC50 determination via fluorescence polarization assays |
Hit validation services | |
• | ELISA- or Luminex-based validation immunoassays |