The gingipains are the major cell-surface proteinases and virulence factors of Porphyromonas gingivalis, considered a keystone pathogen of chronic periodontitis (severe gum disease). We recently showed that these cysteine proteinases prefer to catalyse transpeptidation over hydrolysis and utilise a wide range of amino acids and peptides as acyl acceptors (1). Furthermore, haemoglobin (Hb) was shown to be digested faster in the presence of added peptides implying that transpeptidation was involved in the rate-limiting step which is the initial digestion of the protein. The transpeptidation products include discontiguous Hb peptides suggesting that the pathway of Hb digestion may involve transpeptidation within the Hb structure using the free N-terminus and other N-termini newly created by transpeptidation or hydrolysis events. To investigate this, both circular and linear transpeptidation products were identified in Hb and myoglobin and analysed with respect to their known crystal structures. Partial protein digests were analysed by orbitrap LC-MS/MS. Transpeptidation products were identified by Mascot and custom made transpeptidation databases or alternatively using pLink cross-linking software.