"TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI

Background: Protein-amide proton hydrogen-deuterium exchange (HDX) is used to investigate protein conformation, conformational changes and surface binding sites for other molecules. To our knowledge, software tools to automate data processing and analysis from sample fractionating (LC-MALDI) massspectrometry-based HDX workflows are not publicly available. Results: An integrated data pipeline (Solvent Explorer/TOF2H) has been developed for the processing of LC-MALDI-derived HDX data. Based on an experiment-wide template, and taking an ab initio approach to chromatographic and spectral peak finding, initial data processing is based on accurate mass-matching to fully deisotoped peaklists accommodating, in MS/MS-confirmed peptide library searches, ambiguous masshits to non-target proteins. Isotope-shift re-interrogation of library search results allows quick assessment of the extent of deuteration from peaklist data alone. During raw spectrum editing, each spectral segment is validated in...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Pornpat Nikamanon, Elroy Pun, Wayne Chou, Marek D. Koter, Paul D. Gershon
• Keywords: BMCBI 2007, BMCBI 2008, Manageable Spectral Numbers, Rates Plots, Spectral Segment