title: The 'protein complex proteome' of chloroplasts in Arabidopsis thaliana.
abstract: Here, a first GelMap of the chloroplast "protein complex proteome" of Arabidopsis thaliana is presented. The GelMap software tool allows assigning multiple proteins to gel spots, thereby taking advantage of the high sensitivity of state-of-the-art mass spectrometry systems. Furthermore, the software allows functional annotation of all identified proteins. If applied to a 2D blue native (BN)/SDS gel, GelMap can selectively display protein complexes of low abundance. For the chloroplast GelMap, highly purified organelles were separated by 2D BN/SDS PAGE and spots were automatically detected using Delta 2D software. Within 287 spots, a total of 1841 proteins were identified (on average 6.4 proteins per spot), representing a set of 436 non redundant proteins. Most of these proteins form part of protein complexes. The quality of the map is reflected by its inclusion of a more or less complete set of protein complexes described for chloroplasts in the literature. The GelMap is publically available at www.gelmap.de/arabidopsis-chloro and may be used as a resource for identifying novel protein complexes within any of its functional categories.
  
  
  CONCLUSIONS
  The chloroplast GelMap represents a data resource for the definition of protein complexes in the model plant A. thaliana. It should be useful for in depth understanding of chloroplast biochemistry, as illustrated by the discovery of so far unknown protein complexes. The GelMap is publically available at www.gelmap.de/arabidopsis-chloro.
authors.affiliation: Institute of Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany.
authors.forename: Christof
authors.initials: C
authors.lastname: Behrens
authors.forename: Christian
authors.initials: C
authors.lastname: Blume
authors.forename: Michael
authors.initials: M
authors.lastname: Senkler
authors.forename: Holger
authors.initials: H
authors.lastname: Eubel
authors.forename: Christoph
authors.initials: C
authors.lastname: Peterhänsel
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Braun
mesh_terms: D025181:ATP Synthetase Complexes / Q000378:metabolism; D017360:Arabidopsis / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D002736:Chloroplasts / Q000378:metabolism*; D007091:Image Processing, Computer-Assisted; D010100:Oxygen / Q000737:chemistry; D045332:Photosystem II Protein Complex / Q000378:metabolism; D017510:Protein Folding; D025941:Protein Interaction Mapping; D021381:Protein Transport; D020543:Proteome; D040901:Proteomics; D012984:Software
chemical_list: D029681:Arabidopsis Proteins; D045332:Photosystem II Protein Complex; D020543:Proteome; D025181:ATP Synthetase Complexes; D010100:Oxygen
keywords: Arabidopsis thaliana; BN; Blue native; Chloroplast; DH; GelMap; MS; Protein complex; blue native; dehydrogenase; mass spectrometry