Are There Indeed Spliced Peptides in the Immunopeptidome?

Arie Admon

doi:10.1016/j.mcpro.2021.100099

Abstract

The claims that a large fraction of the immunopeptidome is composed of spliced major histocompatibility complex (MHC) peptides have stirred significant excitement and raised controversy. Here, I suggest that there are likely no spliced peptides in the immunopeptidome, and if they exist at all, they are extremely rare. I base this claim on both biochemical and bioinformatics considerations. First, as a reactant in normal proteolytic reactions, water will compete with transpeptidation, which has been suggested as the mechanism of peptide splicing. The high mobility and abundance of water in aqueous solutions renders transpeptidation very inefficient and therefore unlikely to occur. Second, new studies have refuted the bioinformatics assignments to spliced peptides of most of the immunopeptidome MS data, suggesting that the correct assignments are likely other canonical, noncanonical, and post-translationally modified peptides. Therefore, I call for rigorous experimental methodology using heavy stable isotope peptides spiking into the immunoaffinity-purified mixtures of natural MHC peptides and analysis by the highly reliable targeted MS, to claim that MHC peptides are indeed spliced.

Highlights

Peptide splicing was suggested to contribute to the immunopeptidome. I suggest that this idea should be reconsidered based on new evidences. Both biochemical and bioinformatics considerations argue against peptide splicing
major histocompatibility complex (MHC) class I molecules are expressed on most nucleated cells of vertebrates and present peptides derived from proteolysis of intracellular proteins
MHC class II molecules are expressed on immune cells and present peptides originating from intracellular proteins and from proteins taken up from outside the cells

Summary

Graphical Abstract

In Brief Peptide splicing was suggested to significantly contribute ligands to the immunopeptidome. This article argues that peptide splicing is at most very rare, even if it happens at all. Considerations against peptide splicing are based on bioinformatics calculations related to the analysis of the LCMS/MS data, and on the abundance of water in the cells, which should compete effectively with the transpeptidation reaction, needed for peptide splicing. Peptide splicing was suggested to contribute to the immunopeptidome. I suggest that this idea should be reconsidered based on new evidences. Both biochemical and bioinformatics considerations argue against peptide splicing Peptide splicing was suggested to contribute to the immunopeptidome. I suggest that this idea should be reconsidered based on new evidences. Both biochemical and bioinformatics considerations argue against peptide splicing

Arie Admon*

Findings

CONCLUSIONS