Open search algorithms discover patterns of chemical modifications via LC-MS/MS

Abstract The introduction of “open search” algorithms has enabled many researchers to discern which biological posttranslational modifications are hiding in their LC-MS/MS data. For chemical biologists, these tools are even more essential, since unanticipated side reactions and redox chemistry can dramatically expand the diversity of mass shifts present in these experiments. This guide walks through the steps necessary to employ the MSFragger and Philosopher tool sets and, more importantly, it assists readers in interpreting the results from open search for subsequent database search in MS-GF+. Four different chemical biology investigations are profiled from SCIEX TripleTOF and Thermo Orbitrap-class instruments: an investigation of organophosphate pesticides by Bui-Nguyen et al., an examination of alkylating reagents by Hains and Robinson, a model of acrylamide neurotoxicity by Prats et al., and a test of formalin fixation and paraffin embedding by Buthelezi et al.