title: Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS.
abstract: The characterization of all protein complexes of human cells under defined physiological conditions using affinity purification-mass spectrometry (AP-MS) is a highly desirable step in the quest to understand the phenotypic effects of genomic information. However, such a challenging goal has not yet been achieved, as it requires reproducibility of the experimental workflow and high data consistency across different studies and laboratories. We systematically investigated the reproducibility of a standardized AP-MS workflow by performing a rigorous interlaboratory comparative analysis of the interactomes of 32 human kinases. We show that it is possible to achieve high interlaboratory reproducibility of this standardized workflow despite differences in mass spectrometry configurations and subtle sample preparation-related variations and that combination of independent data sets improves the approach sensitivity, resulting in even more-detailed networks. Our analysis demonstrates the feasibility of obtaining a high-quality map of the human protein interactome with a multilaboratory project.
authors: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors: Markku
authors: M
authors: Varjosalo
authors: Roberto
authors: R
authors: Sacco
authors: Alexey
authors: A
authors: Stukalov
authors: Audrey
authors: A
authors: van Drogen
authors: Melanie
authors: M
authors: Planyavsky
authors: Simon
authors: S
authors: Hauri
authors: Ruedi
authors: R
authors: Aebersold
authors: Keiryn L
authors: KL
authors: Bennett
authors: Jacques
authors: J
authors: Colinge
authors: Matthias
authors: M
authors: Gstaiger
authors: Giulio
authors: G
authors: Superti-Furga
mesh_terms: D002460:Cell Line; D002846:Chromatography, Affinity; D016208:Databases, Factual; D006801:Humans; D016023:Integrins; D007753:Laboratories / Q000592:standards*; D013058:Mass Spectrometry / Q000379:methods* / Q000592:standards*; D046912:Multiprotein Complexes / Q000737:chemistry*; D010770:Phosphotransferases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D060066:Protein Interaction Maps; D015203:Reproducibility of Results
chemical_list: D016023:Integrins; D046912:Multiprotein Complexes; D010770:Phosphotransferases