Improved single-step enrichment methods of cross-linked products for protein structure analysis and protein interaction mapping

Chemical cross-linking/mass spectrometry (MS) is gradually developing into a routine method to investigate protein conformation and to decipher protein interaction networks. To increase identification rates of the frequently low abundant cross-linked products in LC/MS/MS experiments, fast and reliable sample preparation protocols are indispensable. We present simplified solid phase extraction methods using C18/SCX StageTips and mixed-mode OASIS MCX cartridges for a single-step enrichment of cross-linked products prior to LC/MS/MS analysis. Our improved protocols result in 3.5 to 4.6 times higher numbers of cross-link identifications for the model protein bovine serum albumin compared to nonprocessed samples.