Question: Automate peptide lookup / matching in human plasma proteome (http://www.peptideatlas.org/hupo/hppp/) database
0
gravatar for cisek
3.8 years ago by
cisek0
cisek0 wrote:

HUPO, the Human Plasma Proteome, has an online database (http://www.peptideatlas.org/hupo/hppp/), however, there is no current automation for looking up several peptides (batch mode) only one peptide at a time. I have a long list of peptides and would like to match them to the human plasma proteome. It also seems that the links to download the data are also broken. Does anyone know of a way of automating/batch submitting to HUPO, or downloading the data and writing an R script, for example? Or is there a different way to query in batch mode the human plasma proteome? Thanks!!! 

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by cisek0
0
gravatar for ALchEmiXt
3.8 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:
A very very very ugly way to handle this as a last resort (after contacting authors and such...) you could try 'selenium' in for instance a python script. It will simulate a human clicking and browsing and uploading... Used it in the past to download a large set of sequences from a shielded non api database GISAID.
ADD COMMENTlink written 3.8 years ago by ALchEmiXt1.9k
0
gravatar for cisek
3.8 years ago by
cisek0
cisek0 wrote:

Thanks for your comment! I'm afraid that this is WAY beyond our programming capabilities :(

ADD COMMENTlink written 3.8 years ago by cisek0
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