Quantitative Proteomics Reveals Distinct Differences in the Protein Content of Outer Membrane Vesicle Vaccines

At
present, only vaccines containing outer membrane vesicles (OMV)
have successfully stopped Neisseria meningitidis serogroup
B epidemics. These vaccines however require detergent-extraction to
remove endotoxin, which changes immunogenicity and causes production
difficulties. To investigate this in more detail, the protein content
of detergent-extracted OMV is compared with two detergent-free alternatives.
A novel proteomics strategy has been developed that allows quantitative
analysis of many biological replicates despite inherent multiplex
restrictions of dimethyl labeling. This enables robust statistical
analysis of relative protein abundance. The comparison with detergent-extracted
OMV reveales that detergent-free OMV are enriched with membrane (lipo)­proteins
and contain less cytoplasmic proteins due to a milder purification
process. These distinct protein profiles are substantiated with serum
blot proteomics, confirming enrichment with immunogenic proteins in
both detergent-free alternatives. Therefore, the immunogenic protein
content of OMV vaccines depends at least partially on the purification
process. This study demonstrates that detergent-free OMV have a preferred
composition.