Automate peptide lookup / matching in human plasma proteome (http://www.peptideatlas.org/hupo/hppp/) database
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!
2 answers
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.
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