title: Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.
abstract: The ability to reliably and reproducibly measure any protein of the human proteome in any tissue or cell type would be transformative for understanding systems-level properties as well as specific pathways in physiology and disease. Here, we describe the generation and verification of a compendium of highly specific assays that enable quantification of 99.7% of the 20,277 annotated human proteins by the widely accessible, sensitive, and robust targeted mass spectrometric method selected reaction monitoring, SRM. This human SRMAtlas provides definitive coordinates that conclusively identify the respective peptide in biological samples. We report data on 166,174 proteotypic peptides providing multiple, independent assays to quantify any human protein and numerous spliced variants, non-synonymous mutations, and post-translational modifications. The data are freely accessible as a resource at http://www.srmatlas.org/, and we demonstrate its utility by examining the network response to inhibition of cholesterol synthesis in liver cells and to docetaxel in prostate cancer lines.
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Kusebauch
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: David S
authors.initials: DS
authors.lastname: Campbell
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Caroline S
authors.initials: CS
authors.lastname: Chu
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Spicer
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Mi-Youn
authors.initials: MY
authors.lastname: Brusniak
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Slagel
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Sun
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Stevens
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Barbara
authors.initials: B
authors.lastname: Grimes
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: David
authors.initials: D
authors.lastname: Shteynberg
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Hoopmann
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Peter
authors.initials: P
authors.lastname: Blattmann
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA; Center for Infectious Disease Research, Seattle, WA 98109, USA.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Ratushny
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Biognosys AG, 8952 Schlieren, Switzerland.
authors.forename: Oliver
authors.initials: O
authors.lastname: Rinner
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Paola
authors.initials: P
authors.lastname: Picotti
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Christine
authors.initials: C
authors.lastname: Carapito
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Chung-Ying
authors.initials: CY
authors.lastname: Huang
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Meghan
authors.initials: M
authors.lastname: Kapousouz
authors.affiliation: Department of Chemical and Biomolecular Engineering, 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, WA 98109, USA.
authors.forename: Tommy
authors.initials: T
authors.lastname: Tran
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
authors.forename: Emek
authors.initials: E
authors.lastname: Demir
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA; Center for Infectious Disease Research, Seattle, WA 98109, USA.
authors.forename: John D
authors.initials: JD
authors.lastname: Aitchison
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Leroy
authors.initials: L
authors.lastname: Hood
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8006 Zurich, Switzerland. Electronic address: aebersold@imsb.biol.ethz.ch.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA. Electronic address: rmoritz@systemsbiology.org.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
mesh_terms: D022126:Access to Information; D000970:Antineoplastic Agents / Q000627:therapeutic use; D045744:Cell Line, Tumor; D002784:Cholesterol / Q000096:biosynthesis; D030562:Databases, Protein; D000077143:Docetaxel; D005260:Female; D006801:Humans; D020407:Internet; D008099:Liver / Q000187:drug effects; D008297:Male; D009154:Mutation; D011471:Prostatic Neoplasms / Q000188:drug therapy; D020543:Proteome; D012326:RNA Splicing; D043823:Taxoids / Q000627:therapeutic use
chemical_list: D000970:Antineoplastic Agents; D020543:Proteome; D043823:Taxoids; D000077143:Docetaxel; D002784:Cholesterol