title: An open-source computational and data resource to analyze digital maps of immunopeptidomes.
abstract: We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the design of efficient immunotherapies.
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.
authors.forename: Etienne
authors.identifier: http://orcid.org/0000-0003-2770-6970
authors.initials: E
authors.lastname: Caron
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.
authors.forename: Lucia
authors.initials: L
authors.lastname: Espona
authors.affiliation: Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Kowalewski
authors.affiliation: Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.
authors.forename: Heiko
authors.initials: H
authors.lastname: Schuster
authors.affiliation: Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, United Kingdom.
authors.forename: Nicola
authors.initials: N
authors.lastname: Ternette
authors.affiliation: Proteomics Unit, Spanish National Biotechnology Centre, Madrid, Spain.
authors.forename: Adán
authors.initials: A
authors.lastname: Alpízar
authors.affiliation: Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
authors.forename: Ralf B
authors.initials: RB
authors.lastname: Schittenhelm
authors.affiliation: Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
authors.forename: Sri H
authors.initials: SH
authors.lastname: Ramarathinam
authors.affiliation: La Jolla Institute for Allergy and Immunology, La Jolla, United States.
authors.forename: Cecilia S
authors.initials: CS
authors.lastname: Lindestam Arlehamn
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.
authors.forename: Ching
authors.initials: C
authors.lastname: Chiek Koh
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.
authors.forename: Ludovic C
authors.initials: LC
authors.lastname: Gillet
authors.affiliation: Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.
authors.forename: Armin
authors.initials: A
authors.lastname: Rabsteyn
authors.affiliation: Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
authors.forename: Pedro
authors.initials: P
authors.lastname: Navarro
authors.affiliation: Pacific Northwest National Laboratory, Richland, United States.
authors.forename: Sangtae
authors.initials: S
authors.lastname: Kim
authors.affiliation: Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Hong Kong, China.
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.
authors.forename: Theo
authors.initials: T
authors.lastname: Sturm
authors.affiliation: Proteomics Unit, Spanish National Biotechnology Centre, Madrid, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Marcilla
authors.affiliation: La Jolla Institute for Allergy and Immunology, La Jolla, United States.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Sette
authors.affiliation: Institute for Systems Biology, Seattle, United States.
authors.forename: David S
authors.initials: DS
authors.lastname: Campbell
authors.affiliation: Institute for Systems Biology, Seattle, United States.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.affiliation: Institute for Systems Biology, Seattle, United States.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
authors.affiliation: Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
authors.forename: Anthony W
authors.initials: AW
authors.lastname: Purcell
authors.affiliation: Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.
authors.forename: Hans-Georg
authors.initials: HG
authors.lastname: Rammensee
authors.affiliation: Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Stevanovic
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D017951:Antigen Presentation; D000941:Antigens / Q000737:chemistry* / Q000276:immunology*; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D006680:HLA Antigens / Q000378:metabolism; D057166:High-Throughput Screening Assays / Q000379:methods; D013058:Mass Spectrometry / Q000379:methods; D010455:Peptides / Q000737:chemistry* / Q000276:immunology*
chemical_list: D000941:Antigens; D006680:HLA Antigens; D010455:Peptides
keywords: DIA; SWATH-MS; computational biology; human; human leukocytes antigen; immunology; immunopeptidome; systems biology; targeted mass spectrometry