plprot - Tobacco proplastid database

V 2.3

Institute of Plant Sciences - Laboratory of Plant Biotechnology

plprot - Tobacco proplastid database

All data in the plprot tobacco proplastid database are based on shotgun protein identification by 1-D PAGE liquid chromatography tandem mass spectrometry (LC-MS/MS). Raw data were interpreted by the SEQUEST **software and searched against the NCBI non redundant protein database. SEQUEST assignments were manually verified. For details see Baginsky et al. (Journal of Proteome Research 3, 1128-1137.).

For data search and output the relevant fields have to be checked. Fields contain the following information:

- Identifier: Unique "GI" identifier from the NCBI protein database (http://www.ncbi.nlm.nih.gov)
- Accession-No.: Stable accession number of protein entry in the NCBI protein database (http://www.ncbi.nlm.nih.gov)
- Organism: Since the tobacco genome is not completely sequenced, peptides must be identified on the basis of identical peptides form homologues proteins from different organisms in the database. Here, the organisms from which the identification originated is provided.
- Fraction: Serial extraction step from which the protein was identified. Abbreviations are: O- osmotic shock (soluble proteins), U- urea wash (peripheral membrane proteins) and C-chaps solubilization (integral membrane proteins)
- Localization: Prediction or reported function in plastids (Y- chloroplast transit peptide, reported pt- very close homologue has a reported function in plastids, co- putative contaminant)
- Protein: Protein annotation from the NCBI protein database
- Function: Putative function of the identified protein based on the annotation. Proteins were manually assorted into the respective functional category.

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