last update : june 2012
Public data retrieved in march 2010
AT_CHLORO is database dedicated to the chloroplast proteome from Arabidopsis thaliana.
An AMT database gathers protein identifications related to a given biological system. LC-MS/MS analyses performed on a high resolution mass spectrometer are used to generate the AMT database where analytical coordinates (RT = retention time, Mr = molecular weight) of the peptides are stored. Using this analytical information an AMT database is meant to be used for label-free quantification experiments at the scale of the chosen biological system.
The AT_CHLORO database stores information for proteins that have been identified in different sub-fractions obtained from A. thaliana chloroplasts (Ferro et al., 2010). Several types of information can be found in the AT_CHLORO database:
Key features of the AT_CHLORO database
To obtain subplastidial localization, highly purified fractions of envelope, stroma and thylakoids were obtained and spectral counting
was used to classify proteins according to their sub-plastidial localization. Using statistical analysis, the localization of 819 proteins, that are
present in the AT_CHLORO, was determined.
Users can (i) consult the whole database, (ii) retrieve proteins that are localized in a sub-plastidial compartment (xxx) (iii) or
choose a set of proteins with their AGI accession numbers.
Users can customize the display and export the results in xls or PDF files.
Each protein has a dedicated page where all related information can be found, including the AMT specific coordinates (RT, Mr).
List of the features that can be retrieved is described here. Some information were retrieved from TAIR (http://www.arabidopsis.org/) and PPDB (http://ppdb.tc.cornell.edu/) in march 2010.
When using the AT_CHLORO database please cite the following reference :
Ferro M, Brugière S, Salvi D, Seigneurin-Berny D, Court M, Moyet L, Ramus C, Miras S, Mellal M, Le Gall S, Kieffer-Jaquinod S, Bruley C, Garin J, Joyard J, Masselon C, Rolland N. AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins. Mol Cell Proteomics. 2010 Jun;9(6):1063-84. Epub 2010 Jan 10.
The AT_Chloro database was used to explore the subplastidial localization of specific metabolic pathways: