title: Gel-free mass spectrometry analysis of Drosophila melanogaster heads.
abstract: Membrane proteins play key roles in several fundamental biological processes such as cell signalling, energy metabolism and transport. Despite the significance, these still remain an under-represented group in proteomics datasets. Herein, a bottom-up approach to analyse an enriched membrane fraction from Drosophila melanogaster heads using multidimensional liquid chromatography (LC) coupled with tandem-mass spectrometry (MS/MS) that relies on complete solubilisation and digestion of proteins, is reported. An enriched membrane fraction was prepared using equilibrium density centrifugation on a discontinuous sucrose gradient, followed by solubilisation using the filter-aided sample preparation (FASP), tryptic and sequential chymotryptic digestion of proteins. Peptides were separated by reversed-phase (RP) LC at high pH in the first dimension and acidic RP-LC in the second dimension coupled directly to an Orbitrap Velos Pro mass spectrometer. A total number of 4812 proteins from 114 865 redundant and 38 179 distinct peptides corresponding to 4559 genes were identified in the enriched membrane fraction from fly heads. These included brain receptors, transporters and channels that are most important elements as drug targets or are linked to disease. Data are available via ProteomeXchange with identifier PXD001712 (http://proteomecentral.proteomexchange.org/dataset/PXD001712).
authors.affiliation: Department of Pediatrics, Medical University of Vienna, Vienna, Austria.
authors.forename: Jana
authors.initials: J
authors.lastname: Aradska
authors.affiliation: Department of Pediatrics, Medical University of Vienna, Vienna, Austria.
authors.forename: Tanja
authors.initials: T
authors.lastname: Bulat
authors.affiliation: Department of Pediatrics, Medical University of Vienna, Vienna, Austria.
authors.forename: Fernando J
authors.initials: FJ
authors.lastname: Sialana
authors.affiliation: Institute of Pathology, Medical University of Graz, Core Facility Mass Spectrometry, Center for Medical Research, BioTechMed Omics Center Graz, Graz, Austria.
authors.forename: Ruth
authors.initials: R
authors.lastname: Birner-Gruenberger
authors.affiliation: Institute for Clinical Neurobiology, University of Würzburg, Würzburg, Germany.
authors.forename: Buchner
authors.initials: B
authors.lastname: Erich
authors.affiliation: Department of Pediatrics, Medical University of Vienna, Vienna, Austria.
authors.forename: Gert
authors.initials: G
authors.lastname: Lubec
mesh_terms: D000818:Animals; D002499:Centrifugation, Density Gradient; D056148:Chromatography, Reverse-Phase; D029721:Drosophila Proteins / Q000032:analysis*; D004331:Drosophila melanogaster / Q000378:metabolism*; D006257:Head; D008565:Membrane Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry
chemical_list: D029721:Drosophila Proteins; D008565:Membrane Proteins
keywords: Animal proteomics; Drosophila melanogaster; Mass spectrometry; Membrane proteins