Dear RG community,
I am working on a project in which one major phase requires a local blast against a list of all peptides known to be translated in Arabidopsis (not predicted peptides, but only those discovered or confirmed by proteome sequencing), or any other plant and bacterial species.
As far as I understand, neither TAIR (https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FProteins%2FTAIR10_protein_lists) nor pep2pro (http://fgcz-pep2pro.uzh.ch/index.php?pep2pro4all) have such a list. It is even not clear how many peptides have been sequenced in A. thaliana so far.
I would be very grateful for any information that can help me locate such resources for A. thaliana and other organisms.
Thank you.
Igor Kryvoruchko, PhD
Hello Dr. Kryvoruchko,
http://www.proteomexchange.org/ is a public depository of proreomics data. Since data deposition is now required by many reputable journals publishing omics data, this might be the most frequently updated database of experimental proteome. Both raw data and search output in generic format can be found there. Not sure if your favorite species is there, but worth checking. Best wishes.
Hello Dr. Kryvoruchko,
http://www.proteomexchange.org/ is a public depository of proreomics data. Since data deposition is now required by many reputable journals publishing omics data, this might be the most frequently updated database of experimental proteome. Both raw data and search output in generic format can be found there. Not sure if your favorite species is there, but worth checking. Best wishes.
Dear Dr. Romanova,
Thank you very much for directing me to this valuable resource.
There are more than 200 datasets deposited for my species of interest (A. thaliana). There are also numerous datasets for prokaryotes, which helps us even further.
Thank you so much once again.
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