title: Generation of High-Quality SWATH®Acquisition Data for Label-free Quantitative Proteomics Studies Using TripleTOF®Mass Spectrometers.
abstract: Data-independent acquisition is a powerful mass spectrometry technique that enables comprehensive MS and MS/MS analysis of all detectable species, providing an information rich data file that can be mined deeply. Here, we describe how to acquire high-quality SWATH®Acquisition data to be used for large quantitative proteomic studies. We specifically focus on using variable sized Q1 windows for acquisition of MS/MS data for generating higher specificity quantitative data.
authors.affiliation: The Buck Institute for Research on Aging, 1201 Radio Road, Redwood City, 94065, CA, USA.
authors.forename: Birgit
authors.initials: B
authors.lastname: Schilling
authors.affiliation: The Buck Institute for Research on Aging, 1201 Radio Road, Redwood City, 94065, CA, USA.
authors.forename: Bradford W
authors.initials: BW
authors.lastname: Gibson
authors.affiliation: SCIEX, 500 Old Connecticut Path, Framingham, MA, 01701, USA. Christie.Hunter@sciex.com.
authors.forename: Christie L
authors.initials: CL
authors.lastname: Hunter
mesh_terms: D002853:Chromatography, Liquid; D019295:Computational Biology / Q000379:methods*; D040901:Proteomics / Q000379:methods* / Q000592:standards; D012680:Sensitivity and Specificity; D012984:Software; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods; D013223:Statistics as Topic; D053719:Tandem Mass Spectrometry / Q000379:methods
keywords: Data-independent acquisitions; Mass spectrometry; Proteomics; Quantitation; SWATH acquisition; Variable windows