Connexins 46 and 50 combine to form the gap junctions in ocular lens fiber cells. These proteins are known to be modified with fiber cell age; however, limited work has been done to characterize specific lens connexin modifications. In this report, bovine lens membrane proteins were isolated, digested by multiple enzymes, and analyzed by HPLC-tandem mass spectrometry. Automated database searching revealed the locations of both phosphorylation and truncation sites. The results confirmed the full sequence of connexin 46 and 99% of the connexin 50 sequence. Eighteen phosphorylation sites on connexin 50 and nine phosphorylation sites on connexin 46 were identified, all on serine or threonine residues. All but three phosphorylation sites on connexin 50 were located the cytoplasmic C-terminus. All of the truncation sites of connexin 50 were localized in the cytoplasmic C-terminus (region 280-304). Truncation sites in connexin 46 were found in four different regions including: the N-terminus (residue G2), the cytoplasmic loop (residues 121-124), the cytoplasmic C-terminus (residues 251-285), and the distal C-terminus (residues 344-395). In an analysis of dissected lenses some truncation sites were specific to nucleus samples and others were detected in both nucleus and cortex samples.