GDay,
MaxQuant fails when I follow this tutorial. I tried the tool version described in the tutorial and the latest one. Both failed, but with different errors. Here is my history. I got similar issues in Galaxy Australia. Can someone confirm that MaxQuant works with an experiment design template? In December I tested another MaxQuant tutorial, and it was fine, but the job setup was different.
Thank you!
Igor
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Update: it seems MaxQuant works with “Trypsin/P” added into “enzyme” field (tested in Australia, a job is running in Europe). The “enzyme” field is marked as optional on the job setup page, with no default value. Is it an optional or compulsory field?
Another MaxQuant tutorial uses “enzyme”: Trypsin/P
Igor
Hi @igor
I remember this coming up before but I can’t find the prior topic here.
Hi @bjoern.gruening – what do you think? Should we update the tool form or is there something else we could do? Thanks!!
Yes if @igor assumption is true we should fix that. Maybe we can get some input from @foellmelanie or @Pratik_Jagtap ?
Hi @jennaj, hi @bjoern.gruening
Another suspicious thing: it seems the tutorial workflow uses different settings for MaxQuant step than the job setup described in the tutorial. The workflow has two variable modifications and “Trypsin/P” in enzyme field, while none are present in the instruction for MaxQuant setup.
Also, I have an impression that MaxQuant inputs are mixed up in the workflow: collection of raw files is connected to fasta input, while I expect protein_database.fasta for this input. Input box is absent for Parameter Group1 > infiles. I expect collection of raw files for this input.
If someone with expertise in the field can have a look…
I checked only the current MaxQuant version, 2.0.3.0+galaxy0, with enzyme “Trypsin/P”.
A possible fix: add * “enzyme”: Trypsin/P to instruction for MaxQuant setup (assuming that the issue with the current setup does exist).
Thank you for looking into it!
Igor
Update for the workflow: the workflow successfully completed on Galaxy Australia, once I fixed the inputs and changed MaxQuant version to the latest.
Hi Igor, sorry you had so much trouble with the tutorial. We have used the same parameters as “optional” as done in the original software. Indeed the provided workflow is correct with the enzyme and variable modifications added, so I now also added this information to the training material. Thank you for testing and reporting.
Best, Melanie
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Hi Melanie,
Thank you for looking into it. The tutorial is very useful for me.
Can you also check the workflow for the tutorial? it has only two input boxes for MaxQuant (design table and collection with raw file), while the tutorial uses three inputs, including a fasta file with protein sequences. It seems the collection of raw files is mistakenly(?) connected to MaxQuant input for protein sequences.
Not urgent by any means.
Have a great day,
Igor