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Immunopeptidomics

Immunopeptidomics services

At OHMX.bio, we offer advanced immunopeptidomics services designed to characterize and quantify peptides presented by Major Histocompatibility Complexes (MHCs). This powerful approach provides valuable insights into immune-related processes and aids in the discovery of novel biomarkers and therapeutic targets.
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Why immunopeptidomics?

Unlike standard proteomics, which focuses on identifying and quantifying all proteins within a sample, immunopeptidomics specifically examines peptides presented by MHC molecules. These peptides represent the “visible” portion of the immune response, providing direct insights into antigen presentation and immune recognition. This makes immunopeptidomics particularly valuable for cancer immunotherapy, infectious disease research, and autoimmune disease studies.
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Our immunopeptidomics workflow

1. Sample Preparation

Biological samples are processed to isolate MHC-bound peptides through immunoaffinity purification techniques. Typical samples are cell lines, tissue samples and PBMC's or isolated immune cells

2. Mass Spectrometry Analysis

The purified peptides are analyzed using high-resolution mass spectrometry, enabling precise identification and quantification of the presented peptide repertoire.

3. Data Processing & Interpretation

Collected data is processed using state-of-the-art bioinformatics tools to characterize peptide sequences, predict antigenicity, and generate actionable insights. Typical output includes quantification and identity of peptides, peptide length distribution and (implied) motif analysis

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Main applications for immunopeptidomics

The primary utility of immunopeptidomics lies in its ability to directly identify the specific peptide antigens that trigger T-cell responses. This has profound implications across several key research domains:

Oncology and Immuno-Oncology

Immunopeptidomics enables the discovery of tumor-associated antigens (TAAs) and patient-specific neoantigens arising from tumor mutations. These epitopes are prime targets for the development of personalized cancer vaccines, adoptive T-cell therapies (e.g., CAR-T, TCR-T), and immune checkpoint inhibitor biomarkers.

Infectious Disease and Vaccinology

Immunopeptidomics facilitates the rational design of vaccines by identifying the immunodominant epitopes derived from viral or bacterial pathogens that elicit protective T-cell immunity.

Autoimmunity and Transplantation

Immunopeptidomics allows for the characterization of the autoantigen repertoire responsible for pathogenic T-cell activation in autoimmune diseases. Similarly, it can identify alloantigens relevant to graft-versus-host disease in transplantation contexts.

Our immunopeptidomics services are tailored to meet the specific needs of your research, providing high sensitivity and reproducibility throughout the process. Contact us to learn more about how OHMX.bio can support your immunopeptidomics projects.
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FAQ

The primary application of immunopeptidomics is the empirical identification of T-cell epitopes for therapeutic or diagnostic purposes. In immuno-oncology, it is used to discover tumor-associated antigens and neoantigens, which serve as targets for personalized cancer vaccines and adoptive T-cell therapies. In vaccinology and infectious disease research, it identifies immunodominant epitopes from pathogens to enable rational vaccine design. For autoimmune disorders, it is used to define the specific autoantigens that are pathologically targeted by the immune system.
What are the primary applications of immunopeptidomics?
The primary application of immunopeptidomics is the empirical identification of T-cell epitopes for therapeutic or diagnostic purposes. In immuno-oncology, it is used to discover tumor-associated antigens and neoantigens, which serve as targets for personalized cancer vaccines and adoptive T-cell therapies. In vaccinology and infectious disease research, it identifies immunodominant epitopes from pathogens to enable rational vaccine design. For autoimmune disorders, it is used to define the specific autoantigens that are pathologically targeted by the immune system.
The core methodology combines affinity purification with mass spectrometry. The process begins with the biochemical isolation of peptide-MHC (pMHC) complexes from a biological sample using specific antibodies. Peptides are then eluted from the MHC molecules and the resulting peptide mixture is analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The LC-MS/MS platform measures the mass-to-charge ratio and fragmentation patterns of the peptides, enabling the precise determination of their amino acid sequences. Finally, bioinformatic algorithms map these sequences to their source proteins to construct a comprehensive profile of the immunopeptidome.
The raw output from an immunopeptidomics analysis is a large dataset of mass spectra. After processing through a bioinformatic pipeline, the final deliverable is typically a list of identified peptide sequences, each with an associated confidence score. This list includes information on the protein of origin for each peptide and often includes quantitative data, such as peptide intensity or spectral counts, which can be used to estimate the relative abundance of each peptide on the cell surface. Further analysis can predict the MHC allele to which each peptide binds.

Our streamlined workflow ensures an efficient turnaround for immunopeptidomics projects. The process consists of three main phases. The initial sample preparation and MHC-peptide isolation involve several days of precise lab work. The mass spectrometry analysis itself is quite rapid, typically requiring only a few hours per sample. Finally, our specialized bioinformatic software significantly accelerates data processing, allowing for a comprehensive analysis and interpretation to be delivered in a matter of days.

Immunopeptidomic analyses can be combined with various other -omics analyses. Genome sequencing can be used to detect variants of the MHC complex (e.g. using our long-read solutions) while RNAseq and Ribo-Seq can be used to uncover dark antigens. OHMX.bio offers this full pipeline.

Let’s get in touch!

Are you curious about how we can work on your -omics challenges together? Fill out the form below!
Our experts will reply within 2 working days to freely discuss your omics project.

Our publications using immunopeptidomics services

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