Objectives The NCBI gene database and human-transcriptome database for alternative splicing were used to determine the expression of mRNAs for P-B (SMR3B) and variant form of P-B. The translational product from the former mRNA was identified as the protein named P-B, whereas that from the latter has not yet been elucidated. In the present study, we investigated the expression of P-B and its variant form at the protein level. Design To identify the variant protein of P-B, (1) cationic proteins with a higher isoelectric point in human pooled whole saliva were purified by a two dimensional liquid chromatography
(2) the peptide fragments generated from the in-solution of all proteins digested with trypsin separated and analyzed by MALDI-TOF-MS
and (3) the presence or absence of P-B in individual saliva was examined by 15% SDS-PAGE. Results The peptide sequences (I37PPPYSCTPNMNNCSR52, C53HHHHKRHHYPCNYCFCYPK72, R59HHYPCNYCFCYPK72 and H60HYPCNYCFCYPK72) present in the variant protein of P-B were identified. The peptide sequence (G6PYPPGPLAPPQPFGPGFVPPPPPPPYGPGR36) in P-B (or the variant) and sequence (I37PPPPPAPYGPGIFPPPPPQP57) in P-B were identified. The sum of the sequences identified indicated a 91.23% sequence identity for P-B and 79.76% for the variant. There were cases in which P-B existed in individual saliva, but there were cases in which it did not exist in individual saliva. Conclusions The variant protein is produced by excising a non-canonical intron (CC-AC pair) from the 3′-noncoding sequence of the PBII gene. Both P-B and the variant are subject to proteolysis in the oral cavity.