What is PhIP-Seq?
Phage ImmunoPrecipitation Sequencing (PhIP-Seq) is a technology platform that combines oligonucleotide-encoded peptidomes with high-throughput DNA sequencing analysis of phage-displayed libraries. The synthetic oligonucleotide libraries are designed to encode peptide tiles that span a library of protein sequences, resulting in a comprehensive and normalized representation of the encoded peptides, which we refer to as the "peptidome(s)".
Deep DNA sequencing of phage-displayed peptidomes permits the quantification of each peptide's antibody-dependent enrichment, relative to other library peptides, spike-in standards, other antibody-containing samples, and/or negative-control samples lacking antibodies. Sample multiplexing is achieved using bar-coded PCR primers, which are employed during preparation of the sequencing library. This reduces per-sample DNA sequencing costs, enabling the analysis of large sample sets.
Overview of the PhIP-seq methodology (Mohan et al., 2018).
PhIP-Seq Platform in Creative Proteomics
At Creative Proteomics, we provide PhIP-Seq technology to provide comprehensive antibody-binding analysis for our clients. Our platform combines OLS with high-throughput DNA sequencing analysis of phage-displayed libraries. The synthetic oligonucleotide libraries are designed to encode peptide tiles that together span a library of protein sequences, enabling a comprehensive and normalized representation of the encoded peptides.
The reliability and accuracy of our results are of utmost importance to us, which is why we employ state-of-the-art instruments and analytical procedures throughout the entire process. Our team of experts performs sample preparation, DNA sequencing, and data analysis with meticulous attention to detail, utilizing industry-leading equipment and software, thereby ensuring foolproof results.
For sample multiplexing, we utilize bar-coded PCR primers, which contribute significantly towards reducing per-sample sequencing costs. This cost-effectiveness facilitates us in analyzing large sets of samples at a very affordable price, which can be a crucial factor in meeting the varying project sizes and timelines of our clients. To cater to such diverse needs, we offer both manual and automated sample processing.
Our PhIP-Seq platform is an extremely versatile technology that can be applied to numerous sample types, such as serum, plasma, and other biological fluids. This platform enables us to detect and quantify antibodies against a wide range of targets, including entire proteomes, pathogens, and other molecules of interest. The flexibility of our platform empowers us to offer a plethora of services to our clients, some of which include but are not limited to:
- Antibody profiling: Comprehensive analysis of serum antibodies against specific antigens or antigen libraries
- Biomarker discovery: Identification of novel biomarkers for various diseases or conditions by comparing antibody combinations in healthy individuals and patients
- Vaccine development: Evaluate immune responses to vaccine candidates by analyzing antibody combinations before and after vaccination
- Drug discovery: Identification of antibodies that bind to specific drug targets
Advantages of PhIP-Seq
PhIP-Seq has several distinct advantages over other antibody binding assays:
- It is not limited to already cloned proteins and can be expressed recombinantly, making it a more versatile platform for antibody binding assays.
- Compared to protein microarrays, PhIP-Seq is more cost-effective, costing approximately two orders of magnitude less per sample to analyze.
- Peptidomes generated using PhIP-Seq have longer, higher quality peptides compared to peptide microarrays.
Reference
- Mohan, Divya, et al. "PhIP-Seq characterization of serum antibodies using oligonucleotide-encoded peptidomes." Nature protocols 13.9 (2018): 1958-1978.
