About the Hands-on Tutorial
ProteoWizard msConvert has become ubiquitous in the role of generating peak-picked mzML files from raw LC-MS/MS data since its initial publication in 2008. Contemporary QqTOF instruments from Bruker and SCIEX, however, can challenge ProteoWizard in three key aspects: ion mobility separation, peak-picking, and precursor ion charge determination. Fast photochemical oxidation of proteins (FPOP) places considerable demands on identification software as peptides may be oxidized at almost any amino acid residue, and localization of these PTMs to particular amino acids is key to the resolution of this technique. This workshop will illustrate the use of TIMSCONVERT for Bruker and SCIEX MS Data Converter for SCIEX LC-MS/MS FPOP experiments, investigating the mzMLs they create and the identifications they yield. The tutorial will also demonstrate analysis of Thermo RAW data for FPOP experiments using a standard ProteoWizard msConvert workflow.