How to connect identifiers in the mass spectroscopy and string database

Question

[Evergreeen]

Hi,

I have a problem with the identifiers in the mass spectrometry data and the STRING-db. I want to know how to connect these and use information in the project.Can you suggest if there are databases that can translate any of the identifiers in the ms data into ENSP?

Thanks

[David Westergaard]

Your question is very vague. The mass spec identifier depends on the software used to process the data. Which kind of identifer do you have?

[Evergreeen]

Hi, We have MATLAB software...

[David Westergaard]

I'm sorry, but it sounds like you have not made the effort of understanding what your "MATLAB software" is doing. MATLAB is a general programming language, and it is not descriptive of your problem.

Answer 1

[Khader Shameer]

String-db provides an index file to do mapping from major gene/protein databases (Ensembl, Entrez, Uniprot etc).

You can get the files here. You can use this for mapping.

protein.aliases.v9.1.txt.gz (445 Mb)    aliases for STRING proteins: locus names, accessions, descriptions...

Link to file: http://string.embl.de/newstring_download/protein.aliases.v9.1.txt.gz

[David Westergaard]

Friendly note: it's possible to filter by organism, reducing file size by a lot. (the homo sapiens alias file is only 13.7 Mb)

Edit: http://string-db.org/newstring_download/protein.aliases.v9.1/9606.protein.aliases.v9.1.txt.gz - per request.

[Khader Shameer]

Hi David, can you add species specific link here ? Thanks!

Answer 2

[Evergreeen]

Hi,

It is MATLAB software and we need to connect mass spectroscopy identifiers to ENSP identifiers...

Thank you