title: Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms.
abstract: Targeted mass spectrometry comprises a set of methods able to quantify protein analytes in complex mixtures with high accuracy and sensitivity. These methods, e.g., Selected Reaction Monitoring (SRM) and SWATH MS, use specific mass spectrometric coordinates (assays) for reproducible detection and quantification of proteins. In this protocol, we describe how to analyze, in a targeted manner, data from a SWATH MS experiment aimed at monitoring thousands of proteins reproducibly over many samples. We present a standard SWATH MS analysis workflow, including manual data analysis for quality control (based on Skyline) as well as automated data analysis with appropriate control of error rates (based on the OpenSWATH workflow). We also discuss considerations to ensure maximal coverage, reproducibility, and quantitative accuracy.
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, CH-8093, Zurich, Switzerland. hroest@stanford.edu.|Department of Genetics, Stanford University, Stanford, CA, 94305, USA. hroest@stanford.edu.
authors.forename: Hannes L
authors.initials: HL
authors.lastname: Röst
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, CH-8093, Zurich, Switzerland. aebersold@imsb.biol.ethz.ch.|Faculty of Science, University of Zurich, CH-8057, Zurich, Switzerland. aebersold@imsb.biol.ethz.ch.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, CH-8093, Zurich, Switzerland. oschubert@mednet.ucla.edu.|Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA. oschubert@mednet.ucla.edu.
authors.forename: Olga T
authors.initials: OT
authors.lastname: Schubert
mesh_terms: D013058:Mass Spectrometry / Q000379:methods* / Q000592:standards; D010455:Peptides; D040901:Proteomics / Q000379:methods* / Q000592:standards; D011786:Quality Control; D015203:Reproducibility of Results; D000073886:Scientific Experimental Error; D012984:Software; D013223:Statistics as Topic / Q000379:methods*; D014584:User-Computer Interface; D064878:Web Browser; D057188:Workflow
chemical_list: D010455:Peptides
keywords: DIA; Data-independent acquisition; OpenSWATH; SWATH; SWATH MS; SWATH acquisition; Skyline; TRIC aligner; Targeted proteomics; pyProphet