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)
2 answers
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).
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
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Try with corresponding genome annotation package, like
org.Hs.eg.dbfor human.Hello kobipe3!
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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.