title: Characterization of top-down ETD in a travelling-wave ion guide.
abstract: Top-down sequencing methods are becoming increasingly relevant for protein characterization, in particular electron capture (ECD) and electron transfer dissociation (ETD) which allow for extensive backbone cleavage with minimal side reactions. The ability to obtain sequence-specific fragments while maintaining aspects of the higher-order structure, as well as the position of deuterium labels in H/D exchange, has attracted interest from scientists in the field of structural proteomics. Recently, ETD has also been combined with ion mobility on commercially available quadrupole/time-of-flight instruments, and this implementation paves the way to novel structural studies and investigation of the ETD process itself. In the current work, we investigate the use of ETD for fragmentation of standard peptides and proteins and provide a detailed description of the effect of the parameters controlling the time and efficiency of the reaction. We also highlight how the combination with ion mobility separation after electron transfer provides extended analytical benefits, such as assignment of fragments to a specific charge-reduced state of the precursor.
authors.affiliation: Biomolecular & Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium; UA-VITO Center for Proteomics, University of Antwerp, Antwerpen, Belgium.
authors.forename: Frederik
authors.initials: F
authors.lastname: Lermyte
authors.affiliation: Biomolecular & Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium.
authors.forename: Tim
authors.initials: T
authors.lastname: Verschueren
authors.affiliation: Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, UK.
authors.forename: Jeffery M
authors.initials: JM
authors.lastname: Brown
authors.affiliation: Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, UK.
authors.forename: Jonathan P
authors.initials: JP
authors.lastname: Williams
authors.affiliation: UA-VITO Center for Proteomics, University of Antwerp, Antwerpen, Belgium; Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Belgium; Applied Bio & Molecular Systems, Flemish Institute for Technological Research (VITO), Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Valkenborg
authors.affiliation: Biomolecular & Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium; UA-VITO Center for Proteomics, University of Antwerp, Antwerpen, Belgium. Electronic address: frank.sobott@uantwerpen.be.
authors.forename: Frank
authors.initials: F
authors.lastname: Sobott
mesh_terms: D000818:Animals; D002417:Cattle; D044927:Electron-Transferring Flavoproteins / Q000032:analysis* / Q000737:chemistry; D004583:Electrons; D006736:Horses; D013058:Mass Spectrometry / Q000379:methods*; D009211:Myoglobin / Q000032:analysis / Q000737:chemistry; D013373:Substance P / Q000032:analysis / Q000737:chemistry; D025801:Ubiquitin / Q000032:analysis / Q000737:chemistry
chemical_list: D044927:Electron-Transferring Flavoproteins; D009211:Myoglobin; D025801:Ubiquitin; D013373:Substance P
keywords: Electron transfer dissociation; Intact protein mass spectrometry; Ion mobility; Top-down mass spectrometry; Top-down sequencing