Get MW of a protein given a uniprot ID in R
2
2
Entering edit mode
7.3 years ago
kobipe3 ▴ 80

I want to query the molecular weight of multiple proteins from R given uniprot ids. I thought of using biomaRt or UniProt.ws, but didn't see which field I should query.

There are online tools performing the calculation given a uniprot ID (PIR, ExPASy), but you have to manually enter the input and save the output.

I want the MW that appears in UniProt when looking in "Sequences" under Mass (for example for the entry http://www.uniprot.org/uniprot/Q9Z2Y8)

molecular weight R uniprot UniProt.ws biomaRt • 4.4k views
ADD COMMENT
2
Entering edit mode

Be aware that the calculated MW on the UniProt page does not include any PTM's. It is solely based on the AA sequence and may as well include signal peptides.

ADD REPLY
0
Entering edit mode

Try with corresponding genome annotation package, like "org.Hs.eg.db" for human.

ADD REPLY
0
Entering edit mode

Hello kobipe3!

We believe that this post is does not fit the main topic of this site.

Thanks for all the answers

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLY
2
Entering edit mode

Instead of closing your own question, please accept the correct answer(s), you may also vote to say thanks.

ADD REPLY
4
Entering edit mode
7.3 years ago
me ▴ 740

On the uniprot site you can ask for the predicted mass column.

Click on the columns button. click on the check-box labeled mass under the sequence category.

Save, search for your accession using the syntax below and get tab delimited output back.

http://www.uniprot.org/uniprot/?format=tab&query=accession:Q6GZX4&columns=id,entry+name,mass

ADD COMMENT
3
Entering edit mode
7.3 years ago
Neilfws 49k

You can get this information from the TogoWS REST service, starting from UniProt ID. For example, using PROSC_MOUSE (which is the ID, Q9Z2Y8 is the accession):

library(rjson)
library(RCurl)

u <- getURL("http://togows.dbcls.jp/entry/uniprot/PROSC_MOUSE.json")
j <- fromJSON(u)

j[[1]]$sq$MW

# [1] 30049

Conversion from accession to ID should be easy using R/biomaRt (search Biostar for numerous examples).

 

ADD COMMENT

Login before adding your answer.

Traffic: 2121 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6