title: Label-free protein quantification for plant Golgi protein localization and abundance.
abstract: The proteomic composition of the Arabidopsis (Arabidopsis thaliana) Golgi apparatus is currently reasonably well documented; however, little is known about the relative abundances between different proteins within this compartment. Accurate quantitative information of Golgi resident proteins is of great importance: it facilitates a better understanding of the biochemical processes that take place within this organelle, especially those of different polysaccharide synthesis pathways. Golgi resident proteins are challenging to quantify because the abundance of this organelle is relatively low within the cell. In this study, an organelle fractionation approach targeting the Golgi apparatus was combined with a label-free quantitative mass spectrometry (data-independent acquisition method using ion mobility separation known as LC-IMS-MS(E) [or HDMS(E)]) to simultaneously localize proteins to the Golgi apparatus and assess their relative quantity. In total, 102 Golgi-localized proteins were quantified. These data show that organelle fractionation in conjunction with label-free quantitative mass spectrometry is a powerful and relatively simple tool to access protein organelle localization and their relative abundances. The findings presented open a unique view on the organization of the plant Golgi apparatus, leading toward unique hypotheses centered on the biochemical processes of this organelle.
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom.
authors.forename: Nino
authors.identifier: http://orcid.org/0000-0002-5136-9161
authors.initials: N
authors.lastname: Nikolovski
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Shliaha
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom.
authors.forename: Laurent
authors.identifier: http://orcid.org/0000-0002-1520-2268
authors.initials: L
authors.lastname: Gatto
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom pd101@cam.ac.uk k.s.lilley@bioc.cam.ac.uk.
authors.forename: Paul
authors.identifier: http://orcid.org/0000-0001-9270-6286
authors.initials: P
authors.lastname: Dupree
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom pd101@cam.ac.uk k.s.lilley@bioc.cam.ac.uk.
authors.forename: Kathryn S
authors.identifier: http://orcid.org/0000-0003-0594-6543
authors.initials: KS
authors.lastname: Lilley
mesh_terms: D017360:Arabidopsis / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D002853:Chromatography, Liquid; D006056:Golgi Apparatus / Q000378:metabolism*; D013058:Mass Spectrometry; D015388:Organelles / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins