title: SWATH-MS as a tool for biomarker discovery: From basic research to clinical applications.
abstract: In the era of quantitative proteomics, where mass spectrometry plays a pivotal role, in particular associated with the use of data-independent acquisition, it is time to perform an overview of this growing field with special focus on one of the most promising approaches: SWATH-MS, and to present future perspectives for its application as a translational tool. Therefore, a summary of this technique is presented focusing on two key relevant concepts associated with its application in biomarker discovery: the protein library and the individual digital maps concepts. It is also the purpose of this review to document the likely impact of SWATH-MS in both fundamental and translational research including biomarker identification and creation of diagnostic tools. To that end, the two concepts referred above were integrated with ongoing technical developments. Finally, some of the current restrictions for the implementation of SWATH-MS on a large scale are identified, and potential solutions presented, namely protocol standardization combined with the use of the proper standards.
authors.affiliation: CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.|Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal.
authors.forename: Sandra Isabel
authors.initials: SI
authors.lastname: Anjo
authors.affiliation: CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.|Institute for Interdisciplinary Research (III), University of Coimbra, Coimbra, Portugal.
authors.forename: Cátia
authors.initials: C
authors.lastname: Santa
authors.affiliation: CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.
authors.forename: Bruno
authors.initials: B
authors.lastname: Manadas
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000378:metabolism*; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods* / Q000592:standards; D040901:Proteomics / Q000379:methods* / Q000592:standards
chemical_list: D015415:Biomarkers
keywords: Biomarkers; Individual digital maps; Proteome libraries; SWATH-MS; Standardized method