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Nesvilab / PD-Nodes

The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes
http://www.nesvilab.org/PD-Nodes/
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How to assign more than 7 dynamic modifications in MS Fragger PD 2.4 #15

Closed algom closed 3 years ago

algom commented 3 years ago

Dear Developers,

So far I have had really good results with the PD nodes, thank you for your work! I was wondering if there is a way to increase the number of dynamic modifications within the MSFragger node. I can only setup 7, but would like to include a couple more (9 in total). I see that using the FragPipe one can setup up to 16, but I would like to keep the analysis in PD, is it possible to increase the modifications?

Thanks a lot,

Alejandro

anesvi commented 3 years ago

And you are not hitting the memory limit with 7? I think Hui-yin can add more, but I think with 9 mods you will need Split program for sure, which is only available in FragPipe

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Dear Developers,

So far I have had really good results with the PD nodes, thank you for your work! I was wondering if there is a way to increase the number of dynamic modifications within the MSFragger node. I can only setup 7, but would like to include a couple more (9 in total). I see that using the FragPipe one can setup up to 16, but I would like to keep the analysis in PD, is it possible to increase the modifications?

Thanks a lot,

Alejandro

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algom commented 3 years ago

No, I haven't run out of memory, so far with 7 has been running fine although with a computer with large memory. Thus, It would be great to be able to have the option to set up 9.

If possible will be more than happy to test it out.

Alejandro

huiyinc commented 3 years ago

Hi Alejandro,

Sorry for the late reply. We have changed the maximum number of modification up to 16, tested and uploaded the node to our github: https://github.com/Nesvilab/PD-Nodes/releases/tag/1.0.7 Please update the node and feel free to ask is there is any problem. Thanks.

Huiyin

Alejandro Gomez-Auli notifications@github.com 於 2020年9月26日 上午5:47 寫道：



No, I haven't run out of memory, so far with 7 has been running fine although with a computer with large memory. But I am using a labeled approach so would need to include those. Thus, It would be great to be able to have the option to set up 9.

If possible will be more than happy to test it out.

Alejandro

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algom commented 3 years ago

Hi Huiyin,

That's great! I will try it out and report if there are any issues.

Thank you very much.

Alejandro

algom commented 3 years ago

Hi Huiyin,

Do I have to setup something different just installed the version you pointed out but still I can only set up 7 dynamic mods in PD 2.4. I closed PD, deleted the .dll, "scanned" for new features in PD, closed it. Copied the new dll, unblocked it and "scanned" for new features. Restarted PD but MSFragger is visible but I can only setup 7 dynamic mods on the left pane.

Thanks,

Alejandro

huiyinc commented 3 years ago

Hi Alejandro

Thanks for reminding me. I add more dynamic modification options in the parameter panel. Please re-download our MSFragger-PD node from: https://github.com/Nesvilab/PD-Nodes/releases/tag/1.0.7, and feel free to ask if there is any problem. Thanks.

Huiyin

Alejandro Gomez-Auli notifications@github.com 於 2020年9月28日 下午7:38 寫道：



Hi Huiyin,

Do I have to setup something different just installed the version you pointed out but still I can only set up 7 dynamic mods in PD 2.4. I closed PD, deleted the .dll, "scanned" for new features in PD, closed it. Copied the new dll, unblocked it and "scanned" for new features. Restarted PD but MSFragger is visible but I can only setup 7 dynamic mods on the left pane.

Thanks,

Alejandro

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