Does the current standalone version work with public datasets in PRIDE, MassIVE, jPOSTrepo and iProX, or Universal Spectrum Identifiers (USIs) from ProteomeXchange?

[zxseason]

Hi developer,
When I used the proteomics study ID, for example '-b PXD000529', it shows no file associated with the ID. Does the current version works by automatically downloading the proteomics study or is there any additional steps to do that?

Thanks,

[wenbostar]

The data downloading url from the public databases was changed. Could you please try this new version https://drive.google.com/file/d/1_xKW7xYDl3bTZe5WyA57PdFJ0l9MRgKY/view?usp=sharing?

[wenbostar]

This is a known issue and has been fixed ba5d3e5.

[zxseason]

Thank you. BTW do I have to specify the modifications, for example TMT or iTRAQ myself by looking into the detail of the study or it is automatically retrieved by Pepquery from some metadata file?

[wenbostar]

You will need to look at the study to set these parameters based on the experiment.