title: Analysis of the HUPO Brain Proteome reference samples using 2-D DIGE and 2-D LC-MS/MS.
abstract: Within the Human Proteome Organization (HUPO) Brain Proteome Project, a pilot study was launched with reference samples shipped to nine international laboratories (see Hamacher et al., this Special Issue) to evaluate different proteome approaches in neuroscience and to build up a first version of a brain protein database. One part of the study addresses quantitative proteome alterations between three developmental stages (embryonic day 16; postnatal day 7; 8 weeks) of mouse brains. Five brains per stage were differentially analyzed by 2-D DIGE using internal standardization and overlapping pH gradients (pH 4-7 and 6-9). In total, 214 protein spots showing stage-dependent intensity alterations (> two-fold) were detected, 56 of which were identified. Several of them, e.g. members of the dihydropyrimidinase family, are known to be associated with brain development. To feed the HUPO BPP brain protein database, a robust 2-D LC-MS/MS method was applied to murine postnatal day 7 and human post-mortem brain samples. Using MASCOT and the IPI database, 350 human and 481 mouse proteins could be identified by at least two different peptides. The data are accessible through the PRIDE database (http://www.ebi.ac.uk/pride/).
authors.affiliation: Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilian University, Munich, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Fröhlich
authors.forename: Derrick
authors.initials: D
authors.lastname: Helmstetter
authors.forename: Monica
authors.initials: M
authors.lastname: Zobawa
authors.forename: Anna C
authors.initials: AC
authors.lastname: Crecelius
authors.forename: Thomas
authors.initials: T
authors.lastname: Arzberger
authors.forename: Hans A
authors.initials: HA
authors.lastname: Kretzschmar
authors.forename: Georg J
authors.initials: GJ
authors.lastname: Arnold
mesh_terms: D000375:Aging / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D001921:Brain / Q000196:embryology / Q000254:growth & development / Q000378:metabolism*; D002851:Chromatography, High Pressure Liquid; D015180:Electrophoresis, Gel, Two-Dimensional; D005456:Fluorescent Dyes; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008297:Male; D013058:Mass Spectrometry; D051379:Mice; D008810:Mice, Inbred C57BL; D008875:Middle Aged; D008969:Molecular Sequence Data; D010865:Pilot Projects; D020543:Proteome / Q000378:metabolism* / Q000592:standards; D012015:Reference Standards
chemical_list: D005456:Fluorescent Dyes; D020543:Proteome