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Structures of the trifunctional crosslink molecules, pyridinoline, deoxypyridinoline and glucosylgalactosyl‐pyridinoline, have been characterized by positive‐ion liquid secondary‐ion mass spectrometry (LSIMS) and collision‐induced dissociation with scanning‐array four‐sector tandem mass spectrometry. It has been found that: (i) the naturally occurring cations (Cat⁺) are readily desorbed by positive‐ion LSIMS utilizing glycerol + thioglycerol (1:1) as liquid matrix and dominate the spectra, facilitating accurate mass measurement; (ii) changing the matrix to 3‐nitrobenzyl alcohol leaves little evidence of the cation, and (iii) collision‐induced dissociation of the cations (Cat⁺) of pyridinoline, deoxypyridinoline and glucosylgalatosyl‐pyridinoline gives a wealth of fragmentation for structure elucidation. These fundamental studies of tandem mass spectra of the known trifunctional crosslink molecules provided valuable …