Pemphigus is a group of rare autoimmune diseases that causes blistering of the skin and mucous membranes, and includes pemphigus vulgaris (PV) and pemphigus foliaceus (PF). Patients with pemphigus have various combinations of autoantibodies to keratinocyte muscarinic acetylcholine receptor subtype M3 (CHRM3), the secretory pathway Ca2+/Mn2+-ATPase isoform 1 (SPCA1), and desmocollin 3 (DSC3). However, there is still a need to characterize these autoantibodies and optimize their detection for diagnosis and disease monitoring. The inventors now developed an ALBIA for the 3 proteins and successfully detected and quantified the presence of auto-antibodies directed against each of these antigens in pemphigus patients. Furthermore, they showed that detection and quantification of anti-SPCA1 and/or anti-CHRM3 were also associated to a risk of relapse in the first year following the treatment using rituximab as a first-line agent. The present invention thus relates to methods for detecting the presence of said pemphigus-specific autoantibodies.