Development of an LC-MS/MS method for absolute quantification of IgG4 by evaluating dependence on the digestion efficiency using a non-cleavable/dually-cleavable internal calibrator set

The measurement of serum IgG4 levels is mandatory for the diagnosis of IgG4-related disease, but no widely accepted reference material exists due to a lack of consensus on the standard assay. Therefore, we developed here an LC-MS/MS method for absolute quantification of IgG4 in a purified IgG sample, addressing a concern over the reliability depending on the proteolytic digestion efficiency. Our method uses internal calibrator sets containing unique amino acid sequences within IgG4, each of which comprises non-cleavable and dually-cleavable peptides labeled with different numbers of isotopes for mass separation, to determine digestion efficiency. Surrogate peptides generated by trypsin or lysyl endopeptidase digestion were selected based on selectivity, stability, and identifiability. IgG4 quantification using synthetic calibrator peptides showed high precision across the two conditions with different peptidases (relative differences ≤6.1%), even with low digestion efficiencies (<20%), which was within the interday precision under an established condition (% coefficient of variation ≤6.9%, digestion efficiencies >90%, n = 5). These results indicate that the LC-MS/MS method for quantifying IgG4 is robust against digestion efficiency variations and is applicable to validating an IgG4 reference material.