Has anyone had experience submitting proteomics data to ProteomeXchange via PRIDE?
I’m working with mass spectrometry data from multiple sample groups. For each group, I have:
.baf and .mgf files (named consistently based on the Mascot search),
.dat and .mzid files (generated from Mascot),
and a .csv file containing processed quantification results (named according to my sample naming convention).
All files are organized and named consistently per sample/group. However, I’m having trouble uploading them to the PRIDE repository – the upload fails or doesn’t seem to complete, even when using the PX Submission Tool.
Has anyone encountered similar issues? Are there specific naming rules, file dependencies, or best practices for successful submission (especially regarding Mascot-based identifications or including optional CSV files)?
Any help or shared experience would be greatly appreciated!
If you haven't already done so, talk to the PRIDE people.
https://www.ebi.ac.uk/pride/markdownpage/pridesubmissiontool
Talk to your IT people, see if they can figure it out.
We've uploaded a lot of data (thousands of runs) and it does work, but it can be variable.
The tool has also been updated recently, the first time in a number of years.
https://github.com/PRIDE-Archive/px-submission-tool/releases
I find persistence is helpful...
Hi Miroslav,
Another option you have is to use MassIVE at ucsd (University of California, San Diego)
massive.ucsd.edu
For COMPLETE submissions which will result in ProteomeExchange accession number (that is also he number that PRIDE provides), you need the following:
.raw files
.mgf (or peak) files
.mzTab (results) file
The only disadvantage that this route has is the fact that you need an ftp (file transfer portal) to move your large size raw files to the project/account you create. I use FileZilla.
Good luck,
Hediye.
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