I am using the PIT workflow and when I get to the “Extract Hits” part of the workflow, the extract hits output is empty. I am seeing that MS-GF+ matched to peptides in my translated transcriptome (see screenshot) and that some are being pulled out in the post-processing step (screenshot). I select the input for extract hits as mzIdentML and choose the post-processing output (mzid) from my MS-GF+ data. I am trying to determine what my problem is… are no peptides hitting a certain threshold and that is why the extract hits file is empty? Should I include another proteome to catch contaminants if that is all that is in my sample? I am very new to proteomics and am trying to work out this workflow. If anyone can lead me to a very detailed tutorial (i.e. that explains each parameter choice in each of the programs in the PIT workflow), I would very much appreciate it!
Thank you for any help!
Extract Hits file is empty - PIT workflow at https://galaxyproject.org/use/galaxy-integrated-omics-gio/
This group has customized workflows/tools that are novel from other public Galaxy servers.
They do offer several tutorials, please see: https://galaxyproject.org/use/galaxy-integrated-omics-gio/
If that is not enough information, you should contact the administrators/developers that created the workflow/tools. I sent you the email address already in a direct message.
Proteomics tutorials are also hosted by the GTN, but these may not contain the exact tools you are using and not that same custom workflow hosted by the GIO public Galaxy server (as far as I know). You’ll need to compare/review. They may be informative anyway.