title: A repository of assays to quantify 10,000 human proteins by SWATH-MS.
abstract: Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland.
authors.forename: George
authors.initials: G
authors.lastname: Rosenberger
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Ruprecht Karls University of Heidelberg , DE-69117 Heidelberg, Germany.
authors.forename: Ching Chiek
authors.initials: CC
authors.lastname: Koh
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
authors.forename: Tiannan
authors.initials: T
authors.lastname: Guo
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland.
authors.forename: Hannes L
authors.initials: HL
authors.lastname: Röst
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
authors.forename: Petri
authors.initials: P
authors.lastname: Kouvonen
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
authors.forename: Ben C
authors.initials: BC
authors.lastname: Collins
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Molecular and Translational Biomedicine, Competence Centre for Systems Physiology and Metabolic Diseases (CC-SPMD), University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland.
authors.forename: Moritz
authors.initials: M
authors.lastname: Heusel
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
authors.forename: Yansheng
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
authors.forename: Etienne
authors.initials: E
authors.lastname: Caron
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
authors.forename: Anton
authors.initials: A
authors.lastname: Vichalkovski
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
authors.forename: Marco
authors.initials: M
authors.lastname: Faini
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland.
authors.forename: Olga T
authors.initials: OT
authors.lastname: Schubert
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Department of Phytopharmaceuticals (Traditional Pharmacy), School of Pharmacy and Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, 71345-1583 Shiraz, Iran.
authors.forename: Pouya
authors.initials: P
authors.lastname: Faridi
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
authors.forename: H Alexander
authors.initials: HA
authors.lastname: Ebhardt
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
authors.forename: Mariette
authors.initials: M
authors.lastname: Matondo
authors.affiliation: Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay , Hong Kong, China.
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.affiliation: Institute for Systems Biology , Seattle, Washington 98109-5234, USA.
authors.forename: Samuel L
authors.initials: SL
authors.lastname: Bader
authors.affiliation: Institute for Systems Biology , Seattle, Washington 98109-5234, USA.
authors.forename: David S
authors.initials: DS
authors.lastname: Campbell
authors.affiliation: Institute for Systems Biology , Seattle, Washington 98109-5234, USA.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.affiliation: Institute for Systems Biology , Seattle, Washington 98109-5234, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
authors.affiliation: AB SCIEX , Concord, Ontario L4K 4V8, Canada.
authors.forename: Stephen
authors.initials: S
authors.lastname: Tate
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Faculty of Science, University of Zurich , CH-8057 Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D020543:Proteome / Q000737:chemistry; D040901:Proteomics / Q000379:methods
chemical_list: D011506:Proteins; D020543:Proteome