This is a brief tutorial to assist in the development of queries for the Arabidopsis Mitochondrial Protein Database Tutorial
This database, and the proteomic data contained in it for Arabidopsis mitochondria, have been accepted for publication in The Plant Cell, please cite the reference below if you make use of this resource. Citation will greatly aid us in continuing to get financial support for the maintenance and further advance of this resource for the research community.
Heazlewood JL, Tonti-Filippini JS, Gout A, Day DA, Whelan J and Millar AH (2004) Experimental analysis of the Arabidopsis mitochondrial proteome highlights signalling and regulatory components, provides assessment of targeting prediction programs and points to plant specific mitochondrial proteins. Plant Cell 16: 241-256.(PubMed)
1. There are a large number of options that can be selected to define a set for a relational query. So for example you could select proteins with a description (Desc/Comment section) including the word 'malate' and press the Query Database button near the bottom of the page. This yields 42 entries from the entire Arabidopsis protein set (~29000) that have this annotation in names/descriptions or comments. If you then go back and select both malate and 'found' in 'Mitochondria' under the Mitochondrial Proteomics' section then you will see the selection of proteins that have been experimentally identified in mitochondrial proteomic experiments. By further adding 'yeast orthologs' from the Mitochondrial Inparanoid Orthologs section to your search you will then find the 6 entries that mention malate, have been found experimentally and that are putative orthologs of known yeast mitochondrial proteins.
2. In this manner very complex queries can be made to investigate many different questions ranging from expression levels (using EST numbers) to physical location on chromosomes (using loci numbers and chromosome selections) to physical characteristics of proteins (GRAVY, pI, MW) to orthology sets with other eukaryotic mitochondrial sets etc. We have used such queries to derive much of the comparative data highlighted in Heazlewood et al (2004).
3. Under the 'Mitochondrial Proteomics Detailsí section, entries can be further queried by the means of idntification. PAGE inducates that the protein was identified from a gel array, while LC/MS/MS indicates a 'gel-free' procedure was utilized. Further detailed queries can be undertaken on the subset identified by Heazlewood et al (2004), through the number of peptides identified and the MSMS spectral confidence match. The sets referred to as 'The Set:416' and 'groom:377' under this section specifically relate to the sets outlined in Heazlewood et al (2004).
4. Any combination of targeting predictors can be selected to view the mitochondrial predictions based on these programs.
5. The entries retrieved can be listed in a certain order by selecting 'Order Results by' and unwanted or wanted columns of information can be selected in the bottom panel of the relational search page.
6. On any given search results page once you have a list of entries in front of you, you can then click on a AtXgXXXXX number of an entry in the list. This gives you a pseudo flat-file providing more detailed information and dynamic links to TAIR, TIGR, MIPS, MPSS, PlantSpecificDB and insertion line WWW pages on this Arabidopsis locus, so you can rapidly get to any resources of other databases provided about this gene.
7. Under the section 'Functional Groups', mitochondrial specific and a selection of more general groups can be queried e.g. the TCA cycle, Respiratory Chain etc.
Please Note: Due to the dynamic nature of the pages, the back buttons on WWW browsers will not always display selections that were made on the previous page. These selections may need to be re-entered, occasionally and browser dependent, you may need to 'refresh' pages when using the back button.