Immunopeptidomics Services for Cancer Antigen Validation

What Immunopeptidomics Delivers for Antigen validation

Immunopeptidomics is a mass spectrometry–based service that profiles the peptides naturally bound and displayed by MHC/HLA molecules on cancer samples. The workflow captures HLA–peptide complexes from the submitted material, releases the bound peptides, and analyzes them by LC-MS/MS, so the readout describes what is actually presented on the cell surface rather than a bulk protein measurement.

Projects typically start from tumor tissue or cancer cell lines, with HLA class I and class II peptide profiling available depending on sample type and study design. Sample intake and QC, HLA typing or MHC allele context review, replicate depth, and prioritization criteria are all confirmed during scoping, and the engagement closes with a bioinformatics-ready peptide identification report.

Detected HLA-associated peptides can be evaluated further through antigen-specific T cell response assays to investigate immune recognition.

What Our Immunopeptidomics Service Covers

Tumor tissue and Cancer Cell Line Samples

Sample intake and QC for tumor tissue or cancer cell lines, with HLA typing or MHC allele context review to frame the peptide profiling strategy.

HLA Class I and Class II Peptide Profiling

Immunoaffinity capture of HLA–peptide complexes followed by peptide elution and sample cleanup, supporting class I and class II profiling as scoped per project.

LC-MS/MS Acquisition and Database Search

LC-MS/MS acquisition of HLA-bound peptides, with database searching against reference or proteogenomic databases to identify presented peptide sequences.

QC with Replicate Runs and Peptide Confidence

Quality control includes replicate runs and peptide confidence assessment so that reported identifications meet the agreed project criteria.

How an Immunopeptidomics Engagement Works

Sample Intake and HLA Context Review We review your tumor tissue or cancer cell line samples, confirm sample QC, and review HLA typing or MHC allele context to define the profiling scope.

HLA–Peptide Complex Capture HLA–peptide complexes are captured by immunoaffinity enrichment, and the bound peptides are released and cleaned up ahead of mass spectrometry.

LC-MS/MS Acquisition HLA-bound peptides are analyzed by LC-MS/MS, with replicate runs used to support peptide confidence within the agreed QC criteria.

Database Search and Identification Acquired spectra are searched against reference or proteogenomic databases to identify the naturally presented peptide sequences.

What You Receive

Deliverable	Typical Content
HLA-Bound Peptide Identification Report	A bioinformatics-ready report listing peptides identified from MHC/HLA complexes captured from tumor tissue or cancer cell lines, with sequence, charge state, and confidence indicators for each entry.
LC-MS/MS Acquisition Summary	A summary of mass spectrometry acquisition parameters, replicate runs, and run-level QC metrics so the peptide evidence can be reviewed and reproduced within the project scope.
Database Search Results	Peptide-to-spectrum matches searched against reference or personalized proteogenomic databases, delivered as a structured table suitable for downstream bioinformatics review.
Candidate Cancer Antigen Prioritization List	A prioritized shortlist of naturally presented peptides proposed as candidate cancer antigens, with the supporting peptide evidence organized for downstream validation planning.
Sample and QC Documentation	Records of sample intake, HLA typing or MHC allele context review, and replicate-level QC outcomes, provided as scoped in the project statement of work.

Why Choose Our Immunopeptidomics Service

Presentation-Level Evidence, Not Prediction Alone

Our service is built around mass spectrometry detection of peptides that are naturally bound and presented on MHC/HLA molecules. The output is direct evidence that a peptide is displayed on the sample you submitted, which you can pair with the candidate antigen lists your team has already assembled before committing to downstream validation work.

Tumor tissue and Cancer Cell Line Compatibility

Projects can be scoped for tumor tissue specimens or cancer cell lines, with sample intake and QC reviewed before the immunoprecipitation-to-LC-MS/MS workflow begins. HLA class I and class II peptide profiling can be requested depending on the biological question and sample context.

Replicate QC and Confidence-Aware Reporting

Replicate runs and peptide confidence indicators are part of the standard reporting structure, so candidate antigens are presented with the supporting evidence needed for downstream validation decisions. Final depth of QC and reporting is defined per project during scoping.

Prioritized, Bioinformatics-Ready Output

Beyond a peptide list, the engagement delivers a structured view of which naturally presented peptides are proposed as candidate cancer antigens, with the underlying spectral and database-search evidence organized for review. Prioritization criteria and report format are agreed during scoping so the output fits the downstream validation pipeline your team already uses.

Research reference

1. Systematic discovery of neoepitope–HLA pairs for neoantigens shared among patients and tumor types

Nature Biotechnology. 2024. DOI: 10.1038/s41587-023-01945-y.

View article

Ready to validate cancer antigens with naturally presented peptide evidence?

Share your tumor tissue or cancer cell line samples, HLA context, and validation goals. Our team will review feasibility, propose a scoped immunopeptidomics workflow, and outline the peptide identification and prioritization deliverables for your project.

A follow-up plan can include dendritic cell maturation and antigen presentation assays when cellular presentation is the next research question.

Request a project consultation