title: 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions.
abstract: BACKGROUND
  The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional proteomics studies, we have created a resource for the visualization of protein information and proteomic datasets for sequenced natural strains of A. thaliana.
  
  
  RESULTS
  The 1001 Proteomes portal can be used to visualize amino acid substitutions or non-synonymous single-nucleotide polymorphisms in individual proteins of A. thaliana based on the reference genome Col-0. We have used the available processed sequence information to analyze the conservation of known residues subject to protein phosphorylation among these natural strains. The substitution of amino acids in A. thaliana natural strains is heavily constrained and is likely a result of the conservation of functional attributes within proteins. At a practical level, we demonstrate that this information can be used to clarify ambiguously defined phosphorylation sites from phosphoproteomic studies. Protein sets of available natural variants are available for download to enable proteomic studies on these accessions. Together this information can be used to uncover the possible roles of specific amino acids in determining the structure and function of proteins in the model plant A. thaliana. An online portal to enable the community to exploit these data can be accessed at http://1001proteomes.masc-proteomics.org/
authors.affiliation: Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Hiren J
authors.initials: HJ
authors.lastname: Joshi
authors.forename: Katy M
authors.initials: KM
authors.lastname: Christiansen
authors.forename: Joffrey
authors.initials: J
authors.lastname: Fitz
authors.forename: Jun
authors.initials: J
authors.lastname: Cao
authors.forename: Anna
authors.initials: A
authors.lastname: Lipzen
authors.forename: Joel
authors.initials: J
authors.lastname: Martin
authors.forename: A Michelle
authors.initials: AM
authors.lastname: Smith-Moritz
authors.forename: Len A
authors.initials: LA
authors.lastname: Pennacchio
authors.forename: Wendy S
authors.initials: WS
authors.lastname: Schackwitz
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Joshua L
authors.initials: JL
authors.lastname: Heazlewood
mesh_terms: D019943:Amino Acid Substitution; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D018744:DNA, Plant; D030562:Databases, Protein; D010766:Phosphorylation; D020641:Polymorphism, Single Nucleotide; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000235:genetics; D040901:Proteomics; D017422:Sequence Analysis, DNA
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D020543:Proteome