Proteogenomics db search tutorial Search GUI Identification Parameters file not available

1

Hello,

I’m working on the Proteogenomics 2: Database Search tutorial and am on the Search GUI step.
The Search GUI tool (Version 4.0.41) in the usegalaxy.eu instance, seems to require an additional input: Identification Parameters file, which is missing in this tutorial. Instead there are Protein Digestion Options, Precursor options, Protein Modification Options parameters given, which I was not able to find. Is this a case of the tutorial being developed with an older version of the tool which currently has changed input files and options?

Could you please direct me as to how I could adapt the parameters in the current version of the Search GUI tool so that I can proceed with the tutorial.

Bests,
Nirvana

2

I had a similar issue. You can generate the Identification Parameters file with this Galaxy app. It is saved as .par, but is the .json file you need and SearchGUI recognizes it as the correct file.
https://usegalaxy.eu/root?tool_id=ident_params

4

Try using the same version as used in the tutorial for a closer input/parameter match.

How to check tool version? The workflows associated with tutorials is one place. This one uses: Perform protein identification using various search engines and prepare results for input to Peptide Shaker
(Galaxy Version 2.9.0)

How to switch tool version?
https://training.galaxyproject.org/training-material/faqs/galaxy/#tools