Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Research Briefing
  • Published:

Capturing the diversity of protein modifications on presented tumor antigens

Post-translational modifications (PTMs) alter the structure, properties and functions of proteins in all aspects of biology. A new computational pipeline, termed protein modification integrated search engine (PROMISE), reveals the impact these modifications might have on the presentation of cancer antigens to T cells.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Global view of the modified immunopeptidome.

References

  1. Aebersold, R. et al. How many human proteoforms are there? Nat. Chem. Biol. 14, 206–214 (2018). A review of the importance of proteoforms, or alterations to the encoded sequence of proteins, as a source of biological variation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Ramarathinam, S. H. et al. Employing proteomics in the study of antigen presentation: an update. Expert Rev. Proteomics 15, 637–645 (2018). A review of the methods and challenges of discovering non-canonical antigens presented on human leukocyte antigen.

    Article  CAS  PubMed  Google Scholar 

  3. Chick, J. et al. A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides. Nat. Biotechnol. 33, 743–749 (2015). Reveals that adding a variable mass shift to the reference space aids the identification of many modified proteins.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Finn, O. J. & Rammensee, H. G. Is it possible to develop cancer vaccines to neoantigens, what are the major challenges, and how can these be overcome? Neoantigens: nothing new in spite of the name. Cold Spring Harb. Perspect. Biol. 10, (2018) A review of current considerations in designing cancer vaccines.

  5. Bassani-Sternberg, M. et al. Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation. Mol. Cell. Proteomics 14, 658–673 (2015). A look at the immunopeptidome in various cancer cell lines to elucidate principles of antigen presentation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This is a summary of: Kacen, A. et al. Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors. Nat. Biotechnol. https://doi.org/10.1038/s41587-022-01464-2 (2022)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Capturing the diversity of protein modifications on presented tumor antigens. Nat Biotechnol 41, 195–196 (2023). https://doi.org/10.1038/s41587-022-01465-1

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41587-022-01465-1

Search

Quick links

Nature Briefing: Cancer

Sign up for the Nature Briefing: Cancer newsletter — what matters in cancer research, free to your inbox weekly.

Get what matters in cancer research, free to your inbox weekly. Sign up for Nature Briefing: Cancer