Tumor Immunotherapy Target Discovery Services

What Is Immunopeptidomics-Based Tumor Antigen Discovery?

Immunotherapy success depends on selecting the right targets—antigens that are presented by tumor cells and recognized by T cells. Our immunopeptidomics service uses high-precision mass spectrometry to directly capture and sequence the complete set of peptides bound to MHC class I and II molecules on tumor cells. This unbiased approach identifies classical neoantigens, cancer-testis antigens, and non-classical antigen libraries that are often missed by prediction-only methods.

By analyzing real patient tumor samples—including FFPE, fresh-frozen tissues, or cell pellets—we deliver a comprehensive view of the tumor immunopeptidome. Each project integrates sample-specific MHC immunoprecipitation, acid elution of bound peptides, LC-MS/MS acquisition, and database searching to map thousands of eluted peptide sequences. Results are then prioritized through bioinformatic pipelines that rank candidates by binding affinity, expression level, tissue specificity, and potential immunogenicity.

This service is designed for pharma and biotech teams expanding early-stage immuno-oncology pipelines who need experimentally validated antigenic targets beyond those predicted from sequencing data alone. Whether your goal is neoantigen discovery for personalized vaccines or identification of shared tumor-associated antigens for off-the-shelf therapies, direct immunopeptidome analysis provides the molecular evidence to de-risk target selection.

What We Deliver

Comprehensive Immunopeptidome Profiling

Deep coverage of MHC class I and II peptide repertoires from human tumor samples using high-resolution LC-MS/MS.

Neoantigen and Tumor-Associated Antigen Discovery

Identification of mutation-derived neoantigens and shared tumor antigens (e.g., cancer-testis) with confident spectral matching.

Bioinformatic Target Prioritization

Ranked shortlist of antigen candidates with binding predictions, expression context, and tumor selectivity scoring.

Validation Support and Orthogonal Confirmation

Options for targeted mass spectrometry (PRM) or orthogonal confirmation; scope defined during project design to support downstream validation.

How It Works

Tumor Sample Preparation and MHC Immunoprecipitation Start with FFPE, fresh-frozen tissue, or cell pellets. Lysates are subjected to MHC class I and/or II immunoprecipitation using validated antibodies to selectively capture peptide–MHC complexes.

Peptide Elution and LC-MS/MS Acquisition Bound peptides are gently acid-eluted, desalted, and concentrated. Samples are analyzed on high-resolution mass spectrometers with data-dependent acquisition to maximize peptide identification depth.

Database Search and Antigen Identification Raw spectra are searched against protein databases (including tumor-specific variant databases) to identify eluted peptide sequences. Both classical and non-classical antigen classes are reported.

Bioinformatic Prioritization and Reporting Peptide candidates are filtered and ranked using binding affinity algorithms, gene expression data, and tumor/normal expression comparisons. A final report with a prioritized target list and supporting evidence is delivered.

Service Scope

Parameter	Typical Project Scope
Sample Input	Sample input accepts FFPE blocks, fresh-frozen tissue, or cell pellets; the number of samples is scoped per project and cohort size is defined in the project SOW.
MHC Coverage	MHC class I and/or II coverage is selected per project objectives; HLA typing is performed when required for allele-specific analysis.
Antigen Identification Scope	The identification scope includes classical neoantigens, cancer-testis antigens, and non-classical antigen libraries, with database searching against tumor-specific variant calls when provided.
Bioinformatic Prioritization	Bioinformatic prioritization ranks candidates by predicted MHC binding affinity, tumor expression level, tissue specificity, and potential immunogenicity; pipelines are configurable per project.
Validation Support	Options for targeted mass spectrometry (PRM) or orthogonal confirmation; scope defined during project design.

Why Choose This Approach

Direct Peptide Capture from Patient Tumors

Unlike prediction-only methods, our workflow physically elutes and sequences peptides naturally presented on MHC molecules. This provides direct experimental evidence of antigen presentation, avoiding false positives from computational algorithms.

High-Resolution Mass Spectrometry

We employ high-precision LC-MS/MS instrumentation capable of identifying thousands of eluted peptide sequences per sample. This depth enables detection of low-abundance neoantigens and non-canonical peptides that define tumor-specific targets.

Integrated Bioinformatics Pipeline

Peptide identification is paired with a customizable bioinformatics framework that ranks targets by binding affinity, expression context, and tumor selectivity. This reduces the candidate list to actionable, high-confidence targets.

Flexible Sample Input and Project Design

Services are scoped around your program needs—working with FFPE, fresh-frozen, or cell pellets, and selecting MHC class coverage, cohort size, and validation depth. The study design is fit-for-purpose, not one-size-fits-all.

Publication

Immunopeptidomics-guided discovery and characterization of neoantigens for personalized cancer immunotherapy

View article

Ready to Advance Your Immuno-Oncology Pipeline?

Contact our team to discuss your tumor antigen discovery needs. We'll help design a project scope that fits your sample types, target classes, and decision timeline—backed by direct mass spectrometry evidence from patient tumors.

Start a Conversation