Open proccaserra opened 5 years ago
Thanks for the input. Yes, the currently community-accepted open format for proteomics is mzML. In the past, I have used msconvert (http://proteowizard.sourceforge.net/tools/msconvert.html) for this conversion step. I think we should publish the open-format files in addition to the proprietary raw format.
@proccaserra sent info on tools - @sedlyarov will do the conversion and submit to proteomXchange. @ulo looking into accompanying metadata for submission
I submitted the proteomics data to the public ProteomeXchange repository, and made some interesting observations regarding requirements on file formats and metadata:
This repository requires not the raw files in an open format (which would be mzML; as also stated by @proccaserra) but the result files. As we used the ProteomeDiscoverer software, the proprietary result file format is *.pdResult. Fortunately, the software can also export the required mzID format.
Next to generic metadata on the whole data set (project title & description, keywords, sample & data processing protocol), they also require a number of more specific annotations on the sample and method:
Interestingly, the actual experimental factors are entered in a free text field, not requiring any structure or ontology.
@ulo please see: https://github.com/compomics/ThermoRawFileParser
the tool is described in the following manuscript (preprint) https://www.biorxiv.org/content/10.1101/622852v1.full
it would help with the release of the dataset public and for future