MouseScan™ PhIP-Seq Antibody Profiling Service

High-throughput Autoantibody Discovery

Murine proteome epitope-level autoantibody profiling services via T7 phage display and immunoprecipitation sequencing (PhIP Seq)


Epitope-level Antibody Discovery Against the Entire Murine Proteome

MouseScan™ service allows us to analyze preclinical murine samples for the presence of autoantibodies against the full GRCm38.p5 mouse proteome in a single-well assay with quantitative sequencing readouts.

MouseScan PhIP-Seq Library Curation and Production

MouseScan enables simultaneous epitope-level autoantibody profiling against an entire murine proteome via phage display and immunoprecipitation sequencing (PhIP-Seq).

MouseScan PhIP-Seq Library Curation and Production Figure

MouseScan PhIP-Seq Methods and Analysis

MouseScan enables simultaneous epitope-level autoantibody profiling against an entire murine proteome.

MouseScan PhIP-Seq Methods and Analysis Figure

MouseScan™ Service at CDI Labs

Technical Details

The first whole proteome murine autoantibody discovery platform reported; the first available commercially. Each protein in the GRCm38.p5 mouse proteome was downloaded and divided into 62-amino acid peptides with 19-AA overlap. Redundant sequences from identical regions of the different isoforms and homologs were eliminated if they had >95% identity overlap. The final library contains 482,672 unique peptide sequences that represent a full murine proteome of 50,135 proteins and protein isoforms.

This was ordered as an oligonucleotide library, PCR-amplified with adaptors for cloning, and packaged into a T7 phage display vector that was expanded in E. Coli. An aliquot from this library is then reacted with diluted patient serum or other antibody-containing fluid. Bound antibodies are immunoprecipitated with protein A/G beads, the precipitate amplified by PCR, and the sequences quantified by a next-generation sequencing and analysis pipeline that compares patient-sample IP read counts to negative controls with no antibody input (mock IPs) in the context of overall clonal frequency of individual peptides in the parent library. Output data are then created at both the peptide level.

Service Details and Data Deliverables

MouseScan service involves case and control serum or plasma samples. These undergo a protein A/G pulldown assay, PCR amplification, and next-generation sequencing. Raw sequence data are run through a normalization and quantitation pipeline. Raw pipeline counts outputs are then provided to customers alongside normalized hit calls data for all individual 62-mer peptides.

Sample Requirements

Serum or plasma20 μL aliquot per sample
Cerebrospinal fluid (CSF)250 μL aliquot per sample
Other antibodies (IgG monoclonals, B cell supernatants, etc)250 μL aliquot per sample at 0.1 mg/mL concentration
12 sample minimumSold in multiples of x12 samples (i.e., x12, x24, x36, x48 – full rows of a standard 96-well plate), and any number after 48 samples
Cohort balancing (studies bigger > 336 samples)

Individual PhIP-Seq studies are prepared in x96 well plates using aliquots of our phage library; each study requires x48 controls pooled plasma, known polyclonal, and protein A/G beads-only internal control samples per sequencer run (provided free-of-charge). Data are most reproducible within a single sequencer run. Sequencer runs are currently limited to 4x 96-well plates (336 experimental samples + x48 controls per run).

Sample Shipping and Sample Return

We will include shipping details in your quote – you must cover the cost of shipping samples to CDI Labs. Typically, after you receive your report, CDI Labs keeps the remaining samples for two months and then disposes of them. When shipping to us, please let us know if you want the remaining samples returned after the study is complete. Return shipping will be charged.