Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics

Katja Baerenfaller*, Jonas Grossmann, Monica A. Grobei, Roger Hull, Matthias Hirsch-Hoffmann, Shaul Yalovsky, Philip Zimmermann, Ueli Grossniklaus, Wilhelm Gruissem, Sacha Baginsky

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)938-941
Number of pages4
Issue number5878
StatePublished - 16 May 2008


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