title: Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.
abstract: We have assembled a proteome map for Arabidopsis thaliana from high-density, organ-specific proteome catalogs that we generated for different organs, developmental stages, and undifferentiated cultured cells. We matched 86,456 unique peptides to 13,029 proteins and provide expression evidence for 57 gene models that are not represented in the TAIR7 protein database. Analysis of the proteome identified organ-specific biomarkers and allowed us to compile an organ-specific set of proteotypic peptides for 4105 proteins to facilitate targeted quantitative proteomics surveys. Quantitative information for the identified proteins was used to establish correlations between transcript and protein accumulation in different plant organs. The Arabidopsis proteome map provides information about genome activity and proteome assembly and is available as a resource for plant systems biology.
authors.affiliation: Institute of Plant Sciences, ETH (Swiss Federal Institute of Technology) Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland. kbaerenfaller@ethz.ch
authors.forename: Katja
authors.initials: K
authors.lastname: Baerenfaller
authors.forename: Jonas
authors.initials: J
authors.lastname: Grossmann
authors.forename: Monica A
authors.initials: MA
authors.lastname: Grobei
authors.forename: Roger
authors.initials: R
authors.lastname: Hull
authors.forename: Matthias
authors.initials: M
authors.lastname: Hirsch-Hoffmann
authors.forename: Shaul
authors.initials: S
authors.lastname: Yalovsky
authors.forename: Philip
authors.initials: P
authors.lastname: Zimmermann
authors.forename: Ueli
authors.initials: U
authors.lastname: Grossniklaus
authors.forename: Wilhelm
authors.initials: W
authors.lastname: Gruissem
authors.forename: Sacha
authors.initials: S
authors.lastname: Baginsky
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000737:chemistry* / Q000166:cytology / Q000235:genetics* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D015415:Biomarkers / Q000032:analysis; D002478:Cells, Cultured; D019295:Computational Biology; D030541:Databases, Genetic; D035264:Flowers / Q000737:chemistry / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D018517:Plant Roots / Q000737:chemistry / Q000235:genetics; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D012639:Seeds / Q000737:chemistry / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D029681:Arabidopsis Proteins; D015415:Biomarkers; D010455:Peptides; D020543:Proteome