[Question] How can I get the acetylation result?

[NCCparksm]

Hello!

I've been running TMT-integrator on our cancer proteome data samples. After I successfully get the global and phospho data, I wanted to run the acetyl data for getting where K(lysine) is acetylated. In Assigned Modifications of PSM.tsv, I could see lysine acetylation. However, when I've run TMT-integrator in fragpipe/MSfragger I got the error massage like that.

How can I get the acetylation result? or Is there any other workflow in here?

-- Sincerely, Park

fragger - copy_params.txt tmt-integrator-conf - copy.txt

log_2021-08-31_19-26-04.txt annotation.txt

[huiyinc]

Hi,

It seems there is no "K:42.0106" column in your psm.tsv file, as shown below: [image: image.png]

I don't know if there is any setting need to be specified in Philosopher to have the column. Maybe @Felipe Leprevost @.> @Sarah Haynes @.> can help us. Also, please use TMT-Integrator v3.1.0: https://github.com/Nesvilab/TMT-Integrator/releases/tag/3.1.0 for the process.

Feel free to let me know if you have any questions. Thanks!

Huiyin

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

[NCCparksm]

Hi @huiyinc

Thank you for your quick response!

After you recommended, I also used v3.1.0 TMT-integrator then I got the similar error. 😢

I thought there is "K:42.0106" column in my psm.tsv file because when I compared to PSM.tsv in phospho data, I could see the similar pattern in assigned modification column. Therefore I'll attach my part of PSM.tsv that is column of assigned_modification. psm_Assigned Modifications.txt

And I wonder if there is settled acetylation analysis workflow setting in fragpipe/MSfragger.

Thank you for your kind response. 😃

--sincerely Park

[huiyinc]

Hi Park,

If you specify K(42.0106) in mod_tag, TMT-Integrator expects there will be a column of K:42.0106, instead of looking for those modifications in the assigned modification column. I think your TMT-Integrator parameter setting is correct, but the K:420106 column is not in your psm.tsv file. That's why we need Felipe or Sarah's help.

Huiyin

NCCparksm @.***> 於 2021年9月2日 週四 下午4:23寫道：

Hi @huiyinc https://github.com/huiyinc

Thank you for your quick response!

After you recommended, I also used v3.1.0 TMT-integrator then I got the similar error. 😢 [image: cmd2] https://user-images.githubusercontent.com/81598472/131808291-35187b35-e62d-4bef-ae16-ea405d684393.PNG

I thought there is "K:42.0106" column in my psm.tsv file because when I compared to PSM.tsv in phospho data, I could see the similar pattern in assigned modification column. Therefore I'll attach my part of PSM.tsv that is column of assigned_modification. psm_Assigned Modifications.txt https://github.com/Nesvilab/TMT-Integrator/files/7096696/psm_Assigned.Modifications.txt

And I wonder if there is settled acetylation analysis workflow setting in fragpipe/MSfragger.

Thank you for your kind response. 😃

--sincerely Park

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/TMT-Integrator/issues/19#issuecomment-911373722, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA7THVZIQY2QUF6DYBTT74YBZANCNFSM5DF5XJUA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

[NCCparksm]

OK!

Thank you for recommendation :)

I'll mail to Felipe or Sarah about my problem.

Park

[sarah-haynes]

Hi Park, apologies for the slow reply. Can you try version 3.1.0 of TMT-Integrator (pre-release)? If you are running through FragPipe, add the TMTIntegrator-v3.1.0.jar file to the 'tools' directory in the 'fragpipe' folder, and change the name of the file to tmt-integrator-3.1.0.jar. You will also need to set the minimum site probability to 0 for TMT-Integrator. Let me know if those changes work for you.

Sarah

[NCCparksm]

Hi! @sarah-haynes First, I sorry for the delay in replying. I tried 3.1.0 version of TMT-Integrator with your advice and it worked! :) Thank you for your efforts!

Park