title: Mass spectrometric protein maps for biomarker discovery and clinical research.
abstract: Among the wide range of proteomic technologies, targeted mass spectrometry (MS) has shown great potential for biomarker studies. To extend the degree of multiplexing achieved by selected reaction monitoring (SRM), we recently developed SWATH MS. SWATH MS is a variant of the emerging class of data-independent acquisition (DIA) methods and essentially converts the molecules in a physical sample into perpetually re-usable digital maps. The thus generated SWATH maps are then mined using a targeted data extraction strategy, allowing us to profile disease-related proteomes at a high degree of reproducibility. The successful application of both SRM and SWATH MS requires the a priori generation of reference spectral maps that provide coordinates for quantification. Herein, we demonstrate that the application of the mass spectrometric reference maps and the acquisition of personalized SWATH maps hold a particular promise for accelerating the current process of biomarker discovery.
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli-Str.16, 8093 Zurich, Switzerland.
authors.forename: Yansheng
authors.initials: Y
authors.lastname: Liu
authors.forename: Ruth
authors.initials: R
authors.lastname: Hüttenhain
authors.forename: Ben
authors.initials: B
authors.lastname: Collins
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D000595:Amino Acid Sequence; D014408:Biomarkers, Tumor / Q000737:chemistry*; D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods* / Q000592:standards; D009369:Neoplasms / Q000175:diagnosis; D020543:Proteome / Q000737:chemistry; D012015:Reference Standards
chemical_list: D014408:Biomarkers, Tumor; D020543:Proteome