This study develops a method to measure the covalent bonds formed between the side chains and terminal amino acids of beta lactoglobulin (BLG) and selected flavor molecules (benzaldehyde, citral, or allyl isothiocyanate) using electro spray ionization mass spectrometry (ESI/MS) and MS/MS. This technique made it possible to measure increases in molecular weight of BLG as the reaction takes place (BLG+ flavor compound). The observed mass shifts on reaction corresponded to either Schiff’s base or Michael addition reactions between the chosen flavor compounds and BLG. In the case of citral, SDS-PAGE analysis revealed that these reactions lead to protein cross-linking. A proteomic approach using tandem MS to identify the sites of post-translational modification between benzaldehyde and BLG revealed that the lysine groups were the reaction sites. Interestingly, benzaldehyde was found to react with several different lysine groups but never more than one of them per BLG molecule (BLG contains 15 lysine groups/molecule). Furthermore, adducts with benzaldehyde were not observed at two lysine groups. Allyl isothiocyanate was found to react with several sites on each BLG molecule. The ESI/MS methodology in tandem with proteomics yields a detailed view of flavor/BLG interactions that may offer insights on minimizing these undesirable reactions in the future.