title: A draft map of the mouse pluripotent stem cell spatial proteome.
abstract: Knowledge of the subcellular distribution of proteins is vital for understanding cellular mechanisms. Capturing the subcellular proteome in a single experiment has proven challenging, with studies focusing on specific compartments or assigning proteins to subcellular niches with low resolution and/or accuracy. Here we introduce hyperLOPIT, a method that couples extensive fractionation, quantitative high-resolution accurate mass spectrometry with multivariate data analysis. We apply hyperLOPIT to a pluripotent stem cell population whose subcellular proteome has not been extensively studied. We provide localization data on over 5,000 proteins with unprecedented spatial resolution to reveal the organization of organelles, sub-organellar compartments, protein complexes, functional networks and steady-state dynamics of proteins and unexpected subcellular locations. The method paves the way for characterizing the impact of post-transcriptional and post-translational modification on protein location and studies involving proteome-level locational changes on cellular perturbation. An interactive open-source resource is presented that enables exploration of these data.
authors.affiliation: Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.|Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
authors.forename: Andy
authors.initials: A
authors.lastname: Christoforou
authors.affiliation: Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.|Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
authors.forename: Claire M
authors.initials: CM
authors.lastname: Mulvey
authors.affiliation: Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Breckels
authors.affiliation: Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.|Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
authors.forename: Aikaterini
authors.initials: A
authors.lastname: Geladaki
authors.affiliation: Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.|Department of Pharmacology, University of Pretoria, Arcadia 0007, Republic of South Africa.
authors.forename: Tracey
authors.initials: T
authors.lastname: Hurrell
authors.affiliation: Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
authors.forename: Penelope C
authors.initials: PC
authors.lastname: Hayward
authors.affiliation: Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
authors.forename: Thomas
authors.initials: T
authors.lastname: Naake
authors.affiliation: Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
authors.forename: Laurent
authors.identifier: http://orcid.org/0000-0002-1520-2268
authors.initials: L
authors.lastname: Gatto
authors.affiliation: Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95314, USA.
authors.forename: Rosa
authors.initials: R
authors.lastname: Viner
authors.affiliation: Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Martinez Arias
authors.affiliation: Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
authors.forename: Kathryn S
authors.initials: KS
authors.lastname: Lilley
mesh_terms: D000818:Animals; D002458:Cell Fractionation; D007150:Immunohistochemistry; D042541:Intracellular Space / Q000378:metabolism*; D000069550:Machine Learning; D013058:Mass Spectrometry; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000378:metabolism*; D015999:Multivariate Analysis; D039904:Pluripotent Stem Cells / Q000378:metabolism; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D013347:Subcellular Fractions
chemical_list: D020543:Proteome