If the MS study was performed on human proteins, you can do that in 5 steps using neXtProt (www.nextprot.org):

1) create a file with the AC numbers (UniProtKB/Swiss-Prot or neXtProt which only differ from the additonal prefix NX_)

2) Import the list in the list management tool of neXtProt ("My Lists" option in the tool menu).

3) Query neXtProt for all the known human mitchondrial proteins. This can be done with the advanced search with two possibilities: including all the proteins with both SILVER and GOLD evidence that they are mitochondrial:

select distinct ?entry where {

?entry :isoform /:cellularComponent ?loc.

?loc :term /:childOf cv:SL-0173.

}

which retrieve 1563 entries in the current release

Or by restricting to "Gold" quality only:

select distinct ?entry where {

?entry :isoform /:cellularComponent ?loc.

?loc :term /:childOf cv:SL-0173.

?loc :quality :GOLD.

}

which retrieve 1171 entries in the current release

4) Save the results of the query in a list

5) Go to the list management tool and perform a "AND" boolean operation between both lists, the result can be saved in a third list which will contains all the mitochondrial proteins in your MS sample.

Best regards

Amos

Hi Amos,

Thanks for the help and information but the study is for bovine cells.

How can I search for this? Is there any way I can convert my identified proteins identifiers orthologous to human and do the search than reverting it back to bovine.

The easiest way is to load your data set into STRING web tool. Here is the link:

http://string-db.org/

You can use either gene symbol or uniprot IDs for your quantified proteins and enter them in STRING. Use bovine genome as background statistical data set. Then perform a Gene ontology cellular component (GOCC) enrichment. In GOCC there should be various terms associated with mitochondria like "Mitochondria" , "Inner membrane of Microchondria" etc. You should be able to get some raw P-values and FDR values of the enriched GOCC terms. Hope this will work for you. 

Thanks, sajib for the help. but I am interested in searching for mitochondria-specific database not in general. Yes, I had used the STRING it is a very good tool to extract raw information. But I want to search specifically related to Mitochondria like very good example has been suggested by Amos. Anyways thanks for the suggestion.

It will not be trivial to map bovine proteins to the human ones: you can do so in 3 different ways. The best one being the third one:

1) if you have list of UniProtKB entries, those that are in Swiss-Prot (about 7000 of them) will have gene names that are given in "synch" with their human orthologs, so those could be mapped using gene names. For the rest its not trivial: some of the TrEMBL entries will have gene names some other not. 

2) Another way, computationally longer, is to run a blast of all your bovine entries against the human set of UniProtKB/Swiss-Prot entries. Then filter for all best hits with >80% identity on at least 90% of the sequence. Hopefully this would get you a list of orthologous human entries 

3) The third way is to retrieve from your bovine sequence the cross-reference to one of the phylogenomic databases (OMA would be best for your purpose) and for each OMA entry, retrieve the corresponding human protein entry.

Example, if you have a hit to bovine protein Q2KJH1, it contains a xref to OMA: TRLVRHN, which will be linked to human entry P12644, the ortholog.

OMA tries to build orthologous groups so that should be the best solutions, but you will not achieve 100% mapping because:

a) The distance between human and bovine

b) Some complex orthology/paralogy protein groups

Best

Amos