The workflow of openms about proteomics.

Community Extensions OpenMS
#1

Hi, all
Is there about the workflow about proteomics?
I want to use the workflow to analysis the data.
Thank you very much!

#2

Hi!

Yes, there should be some workflows on the KNIME hub:

Which are also described in the KNIME blog:

HTH
Julianus

#3

Thank you very much！

#4

Now I have a question for you?
Where can I download the data in the workflow ?

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#5

Hi,

OpenMS User Tutorial - OpenMS 2.7.0 documentation.

This points to here.

1 Like
#6

Ok,Thank you! I will try it.

#7

@jpfeuffer

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Error: File not found (the file ‘E:\iPRG2015_Hannes\iPRG2015_target_decoy_nocontaminants.fasta.psq’ could not be found)
I dowload the file，but it’s wrong.

#8

I think you downloaded the wrong folder.
It is there: index - powered by h5ai v0.28.1 (https://larsjung.de/h5ai/)

#9

Yes, I am wrong. I dowload the file to test the flow. Thank you!

#10

Yes, the workflow can work. The .fasta, .fasta.pin, .fasta.phr input the inputfile respecticely, Then The worlflow can be flow. So I have a conflusion that The InputFile can contain three files. followed the storage then is excuted. It’s magical!
@jpfeuffer The node ID should contain the nodes(Input files OMSSAAdapter peptideindexer). Is it right?

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#11

@jpfeuffer Hi, the flow occures the error.
Error: Unable to write file (the file ‘F:\KNIME_temporary\knime_openmsLFQ_iPRG245011\fs-IDCon_11-197-45027\000\000\IDConflictResolver_0\JD_06232014_sample2_A.featureXML’ could not be created. invalid file extension, expected ‘consensusXML’)

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#12

Hi, please try to set the OutputType in the configuration dialogue of IDConflictResolver to consensusXML

#13

Yeah，I got it！Thank you very much！