Using a quadrupole ion trap mass spectrometer, trimethyl borate was allowed to react with dihydrogen phosphate, deprotonated O-phosphoserine, and a set of hydrogen bonded complexes involving dihydrogen phosphate and neutral acids (phosphoric acid, acetic acid, serine, and O-phosphoserine). The reactions show a consistent pattern in which the initial attack leads to addition with the loss of one or two CH 3 OH molecules. Collision-activated dissociation (CAD) experiments on the reaction products generally lead to the loss of an additional CH 3 OH molecule. In no case is a partner from the original hydrogen-bonded complex lost. The results indicate that the reactions lead to structures where the phosphate and its complex partner are covalently bound to the boron. For each of the reactions, rate constants were determined. In the course of CAD experiments (up to MS 5 ), several novel borophosphate structures were identified. The work is supported by ab initio calculations on selected species. (J Am Soc Mass Spectrom 2002, 13, 1088 -1098) © 2002 American Society for Mass Spectrometry P hosphates play a key role in biochemistry and the phosphorylation of a peptide is a common mechanism of activation. Phosphates offer opportunities for hydrogen bonding and non-covalent interactions of this type may provide clues to the site of phosphorylation in a peptide as well as the secondary structure of a protein. By their nature, the non-covalent interactions tend to be relatively weak and can be difficult to identify, especially by mass spectrometry. To explore these non-covalent interactions in greater detail, it would be useful to have a reagent that could efficiently convert them into covalent bonds that then could be probed by standard structural methods (i.e., collision-activated dissociation).In this paper, we report the use of trimethyl borate (TMB) as reagent for cross-linking hydrogen-bonded complexes of inorganic and bioorganic phosphates. This compound and related boron reagents have previously been shown by Bowie and co-workers [1,2] to react readily with hydrogen-bonded alcohol/alkoxide complexes to give species where the boron is linked to both components of the original complex. TMB has also been used as a reagent for identifying structural motifs in poly-functional molecules via positive ion mass spectrometry [3,4]. Despite the inherent low reactivity of phosphates in the gas phase [5], we have found that TMB gives rapid reactions that appear to involve the formation of covalent bonds between the partners in the phosphate complexes. As models for more complicated systems, we initially have investigated the reactions of TMB with complexes formed by combining H 2 PO 4 Ϫ with H 3 PO 4 , CH 3 CO 2 H, serine, and O-phosphoserine. In addition, we have studied the reactions of TMB with the hydrogen-bonded dimer complex of O-phosphoserine.