Profiling the autoantibody repertoire with proteome-wide antigen collections is emerging as a powerful tool for the identification of biomarkers for autoimmune diseases. Here, a systematic and undirected approach was taken to screen for profiles of IgG in human plasma from 90 individuals with multiple sclerosis (MS) related diagnoses. Reactivity pattern of 11,520 antigens (corresponding to ~38% of all human protein encoding genes) were generated on planar protein microarrays built within the Human Protein Atlas. IgG reactivity was observed towards more than 2,000 antigens, among which 64% were recognized only in single individuals. Reactivity distributions among MS subgroups were used to select 384 antigens, which were then re-evaluated on planar microarrays, corroborated with suspension bead arrays in a larger cohort (n=376), and confirmed for specificity in inhibition assays. Among the heterogeneous pattern within and across MS subtypes, differences in recognition frequencies were found for 51 antigens, which were enriched for proteins of transcriptional regulation. In conclusion, a strategy on complementary high-throughput protein array platforms facilitated the discovery and verification of disease-associated autoimmunity signatures that are proposed as additional antigens for larger scaled validation across MS biobanks.