Nature Methods | Methagora

PRIDE Converter – A new tool for proteomics

The administrators of the EBI proteomics repository PRIDE have just announced, in the July issue of Nature Biotechnology, the availability of a software tool to facilitate data deposition.

According to Lennart Martens and co-authors, the new tool, PRIDE Converter, “makes it straightforward to submit proteomics data to PRIDE from most common data formats.” This comes handy.

Depositing proteomics data into a structured public repository is a very worthwhile effort—one that Nature Biotechnology, Nature Methods, and other Nature journals strongly encourage. To date, however, the problem has been that in some cases, depositing data remained an effort.

Things could get particularly challenging if you happened to have large datasets in instrument-specific formats. Converting these into the XML-based format needed for data submission required time and informatics skills. Apparently, now, PRIDE Converter does it for you.

Proteomics researchers need effective ways of sharing data. Submission of data to public repositories upon publication should become as automatic in proteomics as it is in some other fields. But realistically, this can only happen if a good infrastructure of databases is in place—it is—and if the submission process is not an undue burden on the researchers.

Kudos to PRIDE, thus, for taking this step in the right direction and for demonstrating a willingness to work with researchers to facilitate submission. It is up to proteomics researchers now, to make use of the tool, and work with its authors to continuously improve it as the field, and their needs, evolve.


There are currently no comments.