N-linked glycosylation is an essential virulence determinant in Campylobacter jejuni, the major causative agent of gastroenteritis in the developed world. Glycosylation is encoded by the pgl gene cluster which encodes for the biosynthesis and attachment of a conserved heptasaccharide glycan to proteins in the C. jejuni periplasm. Over 80 membrane-associated proteins have been identified, however the functional role played by glycan attachment is almost completely unknown. We used quantitative proteomics by label-based and targeted strategies to examine glycosylation negative C. jejuni in comparison to wild-type. These technical approaches were considered as ‘discovery’ (label-based) and ‘validation’ data sets in our subsequent analysis. Inclusion of a glycosylation restored strain enabled us to further exploit the proteomics data to exclude non-specific protein abundance changes that could be considered as off-target effects. These data have provided a reference set of changes associated with protein N-glycosylation that could subsequently be tested by phenotypic analysis to determine the role of this modification in Campylobacter biology.