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Immunopeptidome Profiling

As a trusted contract research organization, Cayman offers a full suite of services supported by our in-house expertise and strategic partnerships with industry leaders. Our immunopeptidome profiling services provide efficient, cost-effective deep sequence analysis of MHC-associated peptides for the identification of neoantigens and potential immunogenic sequences. We’ve partnered with leading industry experts to provide a complete package for clients’ neoantigen discovery needs from isolation and sequencing of MHC-associated peptides to peptide synthesis and production.

  • Identification of thousands of MHC-associated peptides
  • Optimized workflow for MHC Class I and II (human or mouse)
  • Allele-specific studies matched to your specifications
  • Suitable for cells or tumor tissue
  • Analysis using Orbitrap MS and unbiased, deep sequencing of the MHC peptidome
  • Peptide synthesis and production
  • Customized antibody production, cell culture, and bioanalysis services can be tailored to your specific project needs

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The adaptive immune system is equipped to recognize and react to specific threats and holds a memory of previous attacks. Learn how our Immunopeptidome Profiling Services can help you harness this machinery to fight cancer, viral infections, and autoimmune diseases.

Immunopeptidome Profiling Workflow

MHC-specific antibodies are utilized to immunoaffinity purify MHC class I and MHC class II complexes from human tumor tissue, cell lines, and primary cells. Gentle elution conditions collect the MHC-associated peptides, which are then subjected to LC-MS/MS analysis for identification and matched to known sequences. Automation of protein and peptide sample preparation using Agilent’s AssayMAP Bravo Platform enables increased capacity and reduces variability. Up to 96 samples can be processed in a single run, using less antibody and fewer cells to yield high-quality results. MS Bioworks is Cayman’s partner in protein mass spectrometry.

Quality Control

Quality control points in our immunoprecipitation workflow help to provide the highest quality data to our clients. We have developed ELISAs to evaluate the solubilization of the MHC complex in lysates as well as the depletion of that complex after the immunoaffinity isolation step. These quality control points allow us to develop efficient, flexible workflows for a variety of client-led objectives, from identifying neoantigens in tumor cells to probing individual HLA alleles’ presentation patterns and pinpointing immunogenic epitopes of biologic drugs.

MHC Class I and MHC Class II Neoantigen Discovery Neoantigen ID

Genetic mutations in cancer cells can give rise to novel peptide sequences (neoantigens) that can be presented via the MHC-I pathway and potentially recognized by the immune system as foreign. Profiling the immunopeptidome of established tumor cell lines or tumor tissue holds potential for the development of personalized antitumor immunotherapies designed to stimulate a patient’s immune response to neoantigen-derived epitopes.

MAPPs

MHC class II associated peptide proteomics (MAPPs) is of growing importance as a drug development tool for biological therapeutics, as repeated administration can lead to immune-mediated neutralization and reduced long-term efficacy of recombinant protein and engineered antibody-based drugs. Cayman has optimized methods to enhance uptake of biologics by APCs, which combined with specific MHC-II immunoprecipitation, results in improved efficiency in identifying potentially immunogenic epitopes in allele-specific patient subsets.

Neoantigen Discovery Services

Our Neoantigen Discovery Services combine Cayman’s expertise in immunopeptidome profiling with GenScript’s expertise in peptide synthesis to provide you with the complete package for neoantigen candidate discovery and development.

GenScript’s Neoantigen Discovery Services include reliable peptide synthesis for functional screening of neoantigen candidates for personalized cancer vaccine and T cell therapies, personalized cancer vaccine animal testing, and clinical stage vaccine immunogenicity testing. Every peptide request is evaluated using NeoPre™; a bioinformatics algorithm to determine synthetic difficulty and the appropriate synthesis platform (i.e., microwave, liquid-phase, solid-phase). Each peptide undergoes total quality management testing to generate a thorough validation report. Additional library design tools (i.e., alanine scanning, overlapping, Tcell truncation) are available to assist with optimizing peptide sequences.

About Our Partners

MS Bioworks, LLC, is a state-of-the-art protein mass spectrometry services provider based in Ann Arbor, Michigan. They provide mass spectrometry services to researchers in the biological sciences, enabling access to the latest mass spectrometry tools, techniques, and expertise.
GenScript is a global biotechnology group providing gene, peptide, protein, CRISPR, and antibodies to scientists in more than 100 countries. Since its founding in 2002, GenScript has grown exponentially through partnerships with scientists conducting fundamental life science and translational biomedical research, as well as early-stage pharmaceutical development.

Literature

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Khairkhah, N., Owolabi, H., Namvar, A., et al. Identification of molecularly targeted therapy-induced immunopeptidome in diffuse midline glioma (DMG). Neoplasia 73, 101278 (2026).

Bedi, D., Hassan, M., Yirsaw, A., et al. The immunopeptidome of colon cancer cells treated with topoisomerase inhibiting drug reveals differential as well as common endogenous protein sampling and display of MHC I-associated peptides. Mol. Cell. Oncol. 12(1), 2471640 (2025).

Thrift, W.J., Lounsbury, N.W., Broadwell, Q., et al. Towards designing improved cancer immunotherapy targets with a peptide-MHC-I presentation model, HLApollo. Nat. Commun. 15(1), 10752 (2024).

Rana, P.S., Ignatz-Hoover, J.J., Guo, C., et al. Immunoproteasome activation expands the MHC Class I immunopeptidome, unmasks neoantigens, and enhances T-cell anti-myeloma activity. Mol. Cancer Ther. 23(12), 1743-1760 (2024).

Bear, A.S., Nadler, R.B., O'Hara, M.H., et al. Natural TCRs targeting KRASG12V display fine specificity and sensitivity to human solid tumors. J. Clin. Invest. 134(21), e175790 (2024).

Chavez, M., Rane, D.A., Chen, X., et al. Stable expression of large transgenes via the knock-in of an integrase-deficient lentivirus. Nat. Biomed. Eng. 7(5), 661-671 (2023).

Pyke, R.M., Mellacheruvu, D., Dea, S., et al. Precision neoantigen discovery using large-scale immunopeptidomes and composite modeling of MHC peptide presentation. Mol. Cell Proteomics 22(4), 100506 (2023).

Bear, A.S., Blanchard, T., Cesare, J., et al. Biochemical and functional characterization of mutant KRAS epitopes validates this oncoprotein for immunological targeting. Nat. Commun. 12(1), 4365 (2021).