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OpenMS / de.openms.knime

Nodes etc. related to OpenMS
http://www.openms.de
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Adding a custom ptm in OMSSAAdapter #36

Open EAD1994 opened 5 years ago

EAD1994 commented 5 years ago

Hello,

I was wondering if it is possible to add custom post-translational modifications in the OMSSAAdapter node in KNIME, or are we restricted to the only ones that are present in the drop down menu?

Thank You

jpfeuffer commented 5 years ago

Hi, the easiest way is to edit the Custom0 to Custom9 entries in the Knime/plugins/de.openms.[YourOS].[version]/share/OpenMS/CHEMISTRY/unimod.xml and then select then in the Adapter. They are pre-registered.

There is a more flexible solution but it is more complicated.

EAD1994 commented 5 years ago

Hi,

Just a follow up question. Once I edit the custom modification and change its name and other info, should the name change in the Adapter, or will it continue to be displayed as custom?

Thanks

jpfeuffer commented 5 years ago

Hi, Ah please don't change the CUSTOM short name otherwise it probably won't find it. I think you can add synonymes for it though.

jpfeuffer commented 5 years ago

It will then still be displayed as CUSTOM in the dialogue. I am not sure about the resulting peptide sequences right now. If it displays as CUSTOM in the results let me know (this would be suboptimal). We can then fix something inside OpenMS or I can provide you an example workflow on how to pass arbitrary modifications via flow variables. How familiar are you with KNIME?

EAD1994 commented 5 years ago

Hi,

In the resulting peptide table it will still say CUSTOM; however, I did not change the name in the xml editor, I still left it as CUSTOM. I only edited the delta mass of the modification as well as the elemental composition of the PTMs.

Thanks,

Ed

From: jpfeuffer notifications@github.com Sent: Monday, July 15, 2019 5:30:25 AM To: genericworkflownodes/de.openms.knime Cc: Delatoba, Eduardo A; Author Subject: Re: [genericworkflownodes/de.openms.knime] Adding a custom ptm in OMSSAAdapter (#36)

It will then still be displayed as CUSTOM in the dialogue. I am not sure about the resulting peptide sequences right now. If it displays as CUSTOM in the results let me know (this would be suboptimal). We can then fix something inside OpenMS or I can provide you an example workflow on how to pass arbitrary modifications via flow variables. How familiar are you with KNIME?

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