title: A calibration routine for efficient ETD in large-scale proteomics.
abstract: Electron transfer dissociation (ETD) has been broadly adopted and is now available on a variety of commercial mass spectrometers. Unlike collisional activation techniques, optimal performance of ETD requires considerable user knowledge and input. ETD reaction duration is one key parameter that can greatly influence spectral quality and overall experiment outcome. We describe a calibration routine that determines the correct number of reagent anions necessary to reach a defined ETD reaction rate. Implementation of this automated calibration routine on two hybrid Orbitrap platforms illustrate considerable advantages, namely, increased product ion yield with concomitant reduction in scan rates netting up to 75% more unique peptide identifications in a shotgun experiment. Graphical Abstract ᅟ.
authors.affiliation: Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA.|Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Rose
authors.affiliation: Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA.|Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA.
authors.forename: Matthew J P
authors.initials: MJ
authors.lastname: Rush
authors.affiliation: Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA.|Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA.
authors.forename: Nicholas M
authors.initials: NM
authors.lastname: Riley
authors.affiliation: Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA.|Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA.
authors.forename: Anna E
authors.initials: AE
authors.lastname: Merrill
authors.affiliation: Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA.|Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA.
authors.forename: Nicholas W
authors.initials: NW
authors.lastname: Kwiecien
authors.affiliation: Thermo Fisher Scientific, San Jose, CA, USA.
authors.forename: Dustin D
authors.initials: DD
authors.lastname: Holden
authors.affiliation: Thermo Fisher Scientific, San Jose, CA, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Mullen
authors.affiliation: Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Westphall
authors.affiliation: Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA. jcoon@chem.wisc.edu.|Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, 53706, USA. jcoon@chem.wisc.edu.|Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA. jcoon@chem.wisc.edu.
authors.forename: Joshua J
authors.initials: JJ
authors.lastname: Coon
mesh_terms: D002138:Calibration; D007700:Kinetics; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods* / Q000592:standards*; D053719:Tandem Mass Spectrometry / Q000379:methods* / Q000592:standards*
chemical_list: D010455:Peptides
keywords: Calibration; ETD; Ion/ion; Kinetics; Mass spectrometry; Orbitrap; Proteomics