Limma node

Haru Yoshikawa

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Apr 14, 2022, 8:52:31 AM4/14/22

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Dear Gerhard,

Thank you very much for sending me the workflows containing the limma node.

I have some questions below. It would be great if you can give me your suggestion.

1. I tried the workflows you have sent me but some warning messages were shown when the consensus workflow was running and processing was somehow not done correctly. I have attached the log of my searches containing both processing and consensus workflows- could you please see warning messages highlighted on the last page of the consensus workflow? Also it would be great if you can find something that I should correct about parameters.

2. If I want to use both MS Amanda 2.0 and Sequest HT, would a workflow shown at the attached picture be okay?

3. Minimum MS Amanda score at the IMP-apQuant node: how much do you recommend?

Thank you in advance for your kind help!

Best wishes,

Haru

20220331_limma_processingWF_details.docx

20220331_limma_consensusWF_details.docx

sample.png

Gerhard Dürnberger

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Apr 22, 2022, 2:53:04 AM4/22/22

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Dear Haru,

ad 1: for some reason the installation of the required R packages XML and limma does not work. This occurs sometimes and I could not find a solution yet. Can you please opne an R window and run the code linked below. Then the packages are installed and limma should work properly next time.

ad 2: Unfortunately workflows with multiple search engines are not supported by apQuant yet. But this is something we defnitely we want to support in the future. I will let you know when it is supported.

ad 3: internally we use a minimum amanda score of 150 for OT/OT data which is quite conservative. For IT MS2 spectra you can go down to 70. Both will result in a more stringent FDR as this is an additional filtering step.

Kind regards, Gerhard

installPackages4limma.R

Haru Yoshikawa

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Oct 12, 2022, 4:10:44 AM10/12/22

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Dear Gerhard,

I have another question regarding the workflows for limma that you have kindly sent me (please see the attached pics).

I remember you mentioned that 'workflows with multiple search engines are not supported by apQuant yet'. So my question is: could I use Sequest HT instead of MS Amanda 2.0 in this processing workflow? If so, which node/ setting should I change? If you can send me some representative processing/ consensus workflows for this analysis, that would be helpful.

Thank you in advance for your kind help.

Best wishes,

Haru

2022年4月22日金曜日 15:53:04 UTC+9 gerhard.due...@gmail.com:

Processing_lost_conn (1).PNG

Consensus.PNG

Gerhard Dürnberger

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Oct 24, 2022, 6:56:49 AM10/24/22

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Dear Haru,

yes, exchanging the search node is possible. You only have to adapt two parameters in apQuant to allow searches with Sequest HT, see screenshot below.