A combination of MALDI-TOF MS and TOF/TOF collision-induced dissociation (CID) experiments was conducted on toluene diisocyanate (TDI) based carbodiimide and phenyl isocyanate (PI) carbodiimide mixtures to examine their degradation mechanisms and identify "fingerprint" side products associated with each of their synthesis. Findings include the first observance of the 3-methyl-1-phenyl-2-phospholene-1-oxide (MPPO)/carbodiimide (CDI) catalyst-attached intermediate and the use of CID fragmentation to verify its chemical structure and degradation processes. This work is significant for two reasons: (1) it identifies extensive branching as the root-cause of viscosity build-up in carbodiimides and (2) it presents a BF3-initiated mechanism leading to polyguanidine formation.