One-Stop Immunopeptidomics Service Solution
- Identify personalized neoantigens for cancer vaccine development or TCR-T cell therapy.
- Construct disease-associated antigen repertoires for autoimmune or infectious disease research.
- Elucidate the rules governing antigen processing and MHC-restricted presentation, deepening understanding of immune recognition.
- Non-enzymatic peptides: Natural peptides are not generated by trypsin digestion, complicating mass spectrometry analysis.
- Short or variant peptides: MHC-restricted peptides often carry mutations or modifications, requiring high-resolution detection.
- Complex sample backgrounds: Non-specific protein interference is particularly significant in tissue samples.
- MHC subtype diversity: Variability in MHC alleles between individuals affects peptide presentation profiles.
In cutting-edge studies such as cancer immunotherapy, personalized vaccine development, and the investigation of autoimmune disease mechanisms, immunopeptidomics serves as a key technology bridging basic immunology research and clinical translation. By analyzing antigenic peptides presented by major histocompatibility complex (MHC) molecules using high-resolution mass spectrometry, immunopeptidomics enables researchers to uncover the molecular mechanisms underlying intracellular antigen processing and immune recognition. Immunopeptidomics focuses on endogenous and exogenous short peptides loaded onto MHC molecules, which are typically of very low abundance, structurally diverse, and strongly influenced by the diversity of MHC alleles. These characteristics impose stringent requirements on experimental design, sample preparation, mass spectrometry sensitivity, and data analysis.
Immunopeptides
Immunopeptides are peptides presented on the cell surface by MHC molecules for recognition by T cells. The presentation pathways differ slightly depending on the MHC class:
MHC Class I: Primarily presents intracellular endogenous antigens, such as tumor antigens or viral proteins, to CD8+ T cells, with typical peptide lengths of 8-11 amino acids.
MHC Class II: Presents exogenous antigens to CD4+ T cells, with peptide lengths typically ranging from 13-25 amino acids.
By comprehensively capturing these antigen peptides and identifying them through high-resolution mass spectrometry, researchers can:
One-Stop Immunopeptidome Service Workflow
1. Sample Processing and MHC Immunoenrichment
A major challenge in immunopeptidomics is the extremely low abundance of target peptides. Efficient and specific enrichment of MHC molecules is therefore essential for success.
(1) Immunoprecipitation (IP) of cell lysates using anti-HLA antibodies to enrich MHC molecules efficiently.
(2) Antibody panels supporting various subtypes, including HLA-A, HLA-B, HLA-C, and HLA-DR.
(3) Compatible with multiple sample types, including tissues, cell lines, PBMCs, and body fluids.
2. Antigen Peptide Elution and Purification
MHC-bound peptides are released under acidic or mild basic conditions, followed by C18 solid-phase extraction (SPE) to remove impurities and background proteins, ensuring high purity and recovery for mass spectrometry analysis.
3. High-Resolution LC-MS/MS Analysis
(1) High-sensitivity mass spectrometry platforms such as Orbitrap Exploris 480, combined with advanced ion mobility technologies like FAIMS Pro, enhance the detection of low-abundance peptides.
(2) Supports both DDA (Data Dependent Acquisition) and DIA (Data Independent Acquisition) modes to accommodate various research objectives.
(3) Mass spectrometry scanning parameters are optimized for short peptides, improving fragment ion mass accuracy and isotope resolution.
4. Bioinformatics Analysis and Antigen Annotation
The value of immunopeptidome data lies in its bioinformatic interpretation. A full analytical workflow, from basic annotation to advanced prediction, includes:
(1) Matching peptides to reference proteomes to infer their source proteins.
(2) Predicting peptide-MHC binding affinities using tools such as NetMHCpan, IEDB, and DeepHLApan.
(3) Neoantigen screening, identification of mutant peptides, and antigen prioritization scoring.
(4) GO and KEGG pathway enrichment analyses, integrated with disease databases for functional annotation.
Technical Challenges: Why Is Immunopeptidomics Difficult?
The core challenge in immunopeptidomics is enriching and identifying low-abundance peptides from complex biological backgrounds, which imposes high demands on both technological platforms and data analysis capabilities:
Standardized enrichment workflows, high-sensitivity mass spectrometry platforms, and precise data decoding algorithms are therefore critical for successful immunopeptidomics.
As a key platform linking antigen recognition with immune response mechanisms, immunopeptidomics continues to drive advances in precision immunology. The accuracy of experimental design, sensitivity of data acquisition, and depth of analysis collectively determine research quality. MtoZ Biolabs, with years of expertise in proteomics and mass spectrometry, is committed to empowering scientific discovery through technological innovation. We provide comprehensive, high-quality immunopeptidome services, supporting researchers with rigor, professionalism, and collaborative expertise. Contact us for technical information or customized service plans to maximize the value of your data and enhance the depth of your discoveries.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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