Question: How to connect identifiers in the mass spectroscopy and string database
0
gravatar for Evergreeen
4.3 years ago by
Evergreeen0
Sweden
Evergreeen0 wrote:

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

 

ADD COMMENTlink modified 3.8 years ago by Biostar ♦♦ 20 • written 4.3 years ago by Evergreeen0

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?

ADD REPLYlink written 4.3 years ago by David Westergaard1.4k

Hi, We have MATLAB software...

ADD REPLYlink written 4.3 years ago by Evergreeen0
1

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.

ADD REPLYlink written 4.3 years ago by David Westergaard1.4k
0
gravatar for Khader Shameer
4.3 years ago by
Manhattan, NY
Khader Shameer18k wrote:

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... 
ADD COMMENTlink written 4.3 years ago by Khader Shameer18k
1

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. 

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by David Westergaard1.4k

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

ADD REPLYlink written 4.3 years ago by Khader Shameer18k
0
gravatar for Evergreeen
4.3 years ago by
Evergreeen0
Sweden
Evergreeen0 wrote:

Hi,

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

Thank you

ADD COMMENTlink written 4.3 years ago by Evergreeen0
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