Immunopeptidomics is a mass spectrometry–based approach that identifies peptides presented by MHC (HLA) molecules on the cell surface. It is uniquely relevant because it reveals directly which antigens are displayed to T cells, rather than inferred from gene expression or in‑silico predictions. By directly linking the proteome to immune recognition, immunopeptidomics enables more reliable target discovery, validation, and prioritization in cancer immunotherapy, autoimmunity, and vaccine research.
Biognosys’ Immunopeptidomics service provides comprehensive characterization of peptides presented by MHC class I and II molecules, enabling direct insight into antigens driving immune recognition. Using an optimized, high‑throughput workflow, the service delivers reproducible identification and quantification of immunopeptides from minimal sample material. It supports deep, unbiased discovery as well as downstream target validation, enabling identification of neoantigens, tumor‑associated antigens, and immune‑modulating targets to accelerate development of personalized cancer immunotherapies, vaccines, and cell‑based therapies in both standalone and large‑scale studies.
Relative quantification of presented MHC class I and II peptidomes across human and mouse models.
Hybrid assay for absolute quantification of presented antigens.
Flexible pulldown strategies and custom pulldown development.
Increased coverage using DIA instead of DDA.
Discovery and targeted quantification under one roof.
In-house application specific software development.
Experts in pulldown optimization and development of custom pulldowns.
1. Native Lysis
Proprietary lysis buffer is paired with a matrix-specific homogenization.
2. Enrichment of MHC-bound Peptides
Cleared lysates are incubated with the relevant MHC-specific antibody-bead complex.
3. Magnetic Separation
Semi-automated washing for better reproducibility.
4. Elution and Clean-up
Peptides are eluted in a mild acidic environment, followed up by several clean-up steps for optimal sample performance.
5. MS Analysis
Instrument and MHC class optimized methods and gradient for industry leading results.
Proteomics Service
MHC class I molecules are expressed on nearly all nucleated cells and present peptides (typically 8–12 amino acids) derived from intracellular proteins, allowing CD8⁺ cytotoxic T cells to recognize infected or malignant cells. In contrast, MHC class II molecules are restricted to professional antigen‑presenting cells and display longer peptides (13–25 amino acids) originating from extracellular proteins processed via endocytosis, driving CD4⁺ T cell responses that orchestrate broader immune reactions.
Both MHC class I and II peptidomes are of high therapeutic relevance. Profiling MHC‑I supports cancer vaccine development, neoantigen discovery, and TCR‑T cell therapy target identification, while MHC‑II profiling is increasingly applied to understand anti‑drug immune responses, autoimmune disease mechanisms, and the development of safer biologics.
Biognosys enables simultaneous relative quantification of MHC class I and class II peptidomes from the same minimal sample input, requiring as little as 15 mg of fresh frozen tissue or 20 million cells. The platform delivers unbiased, label‑free quantification across samples and experimental conditions, allowing robust comparison of peptide presentation within and between studies. This integrated approach provides a comprehensive view of antigen presentation with high sensitivity and reproducibility.
Peptides are isolated using pan‑allele antibody‑based immunoprecipitation, including W6/32 for human HLA class I, IV12 for pan‑HLA class II, and equivalent antibodies for mouse H‑2 and I‑A/I‑E complexes. Enriched peptides are analyzed using data‑independent acquisition (DIA) mass spectrometry, with quantitative analysis performed in Spectronaut. The combination of pan‑allele capture, minimal input requirements, and DIA‑based quantification enables a single, reproducible workflow for both MHC classes and across species.
Proteomics Service
Targeted immunopeptidomics enables precise, quantitative measurement of selected MHC‑presented peptides when confidence and sensitivity are paramount. Following enrichment of MHC class I or class II ligands, predefined peptides of interest are measured with amino‑acid resolution, allowing discrimination of sequence variants, mutations, and post‑translational modifications.
Using stable isotope‑labeled reference peptides as internal standards, targeted assays provide absolute quantification of endogenous peptide abundance and enable estimation of copy number per cell for single peptides or in a highly multiplexed format.
With femtomolar‑level sensitivity Targeted Immunopeptidomics supports validation of antigen presentation across samples, treatments, and species. This approach is ideally suited for target confirmation, biomarker validation, and translational decision‑making from preclinical models through clinical development.
Proteomics Service
Optimized workflows include robust pan‑allele MHC class I enrichment as well as an optimized HLA‑A*02:01 pulldown using the BB7.2 antibody, targeting the most prevalent HLA allele in Caucasian populations.
Unbiased profiling of MHC class II peptides presented by HLA‑DR, HLA‑DP, and HLA‑DQ enables deep characterization of CD4⁺ T‑cell–relevant antigens. Powered by DIA mass spectrometry and advanced bioinformatics, this approach supports reproducible comparison of healthy versus diseased tissue, treated versus untreated models, and human and preclinical samples within a unified discovery workflow.
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