Empty TMT Integrator outputs

[vinayakvsv]

Hello,

I have been running TMT-integrator on CPTAC CCRCC proteomic data samples 01CPTAC_CCRCC_Proteome_JHU_20171007 and 02CPTAC_CCRCC_Proteome_JHU_20171003 (as described in the tutorial). I have successfully run TMT-integrator through the Philosopher pipeline mode and separately on the psm.tsv outputs. However, my TMT-Integrator .tsv outputs are empty -- I only get headers. I have seen previous threads on this issue, and even after I filled in the empty Mapped Genes column with entries from the Entry Name column, I still get empty output files.

I am running the TMT-integrator JAR file stored in a separate location. Attached is my .yml file for TMT-integrator and the two annotation.txt files that I supplied for the CCRCC samples. Philosopher otherwise runs fine.

Please let me know how I can fix this issue. Thanks.

--Vinay

TMT_integrator.v2.yml.txt annotation.txt annotation.txt

[huiyinc]

Hi Vinay,

Can you please send me your TMT-Integrator parameter file (i.e., the yml file)? Thanks.

Huiyin

vinayakvsv @.***> 於 2021年5月30日 週日 下午3:09寫道：

Hello,

I have been running TMT-integrator on CPTAC CCRCC proteomic data samples 01CPTAC_CCRCC_Proteome_JHU_20171007 and 02CPTAC_CCRCC_Proteome_JHU_20171003 (as described in the tutorial). I have successfully run TMT-integrator through the Philosopher pipeline mode and separately on the psm.tsv outputs. However, my TMT-Integrator .tsv outputs are empty -- I only get headers. I have seen previous threads on this issue, and even after I filled in the empty Mapped Genes column with entries from the Entry Name column, I still get empty output files.

I am running the TMT-integrator JAR file stored in a separate location. Attached is my .yml file for TMT-integrator and the two annotation.txt files that I supplied for the CCRCC samples. Philosopher otherwise runs fine.

Please let me know how I can fix this issue. Thanks.

--Vinay

TMT_integrator.v2.yml.txt https://github.com/Nesvilab/TMT-Integrator/files/6565841/TMT_integrator.v2.yml.txt annotation.txt https://github.com/Nesvilab/TMT-Integrator/files/6565842/annotation.txt annotation.txt https://github.com/Nesvilab/TMT-Integrator/files/6565843/annotation.txt

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

[vinayakvsv]

Hello Huiyin,

I attached it to my previous message -- it is TMT_integrator.v2.yml.txt (I had to add the txt extension so that I could upload it to Github).

Thanks for the speedy reply! --Vinay

[huiyinc]

Hi Vinay,

The yml file looks fine. Can you please send me a PSM table? You can email to: @.***, if the file size is too large. Thank you.

Huiyin

vinayakvsv @.***> 於 2021年5月30日 週日 下午3:13寫道：

Hello Huiyin,

I attached it to my previous message -- it is TMT_integrator.v2.yml.txt (I had to add the txt extension so that I could upload it to Github).

Thanks for the speedy reply! --Vinay

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

[vinayakvsv]

Hello Huiyin,

Here is a dropbox link to 01CPTAC_CCRCC_Proteome_JHU_20171007 https://www.dropbox.com/s/gptf8hndpcgifn0/psm.tsv?dl=0 The Mapped Gene column is empty, so I filled them in for philosopher. Otherwise, the rest of the .tsv is the same.

--Vinay

[huiyinc]

Hi Vinay,

I notice that the values in the Intensity column are all 0. Do you run FreeQuant command in Philosopher? Thanks.

Huiyin

vinayakvsv @.***> 於 2021年5月30日 週日 下午3:43寫道：

Hello Huiyin,

Here is a dropbox link to 01CPTAC_CCRCC_Proteome_JHU_20171007 https://www.dropbox.com/s/gptf8hndpcgifn0/psm.tsv?dl=0 The Mapped Gene column is empty, so I filled them in for philosopher. Otherwise, the rest of the .tsv is the same.

--Vinay

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

[vinayakvsv]

Hello Huiyin,

Not that I am aware. The option in the yml file that matches it is

# grep -i "FreeQuant" philosopher.yml
Label-Free Quantification:                       # Freequant

Should I specify a "yes/no" value in this option to run Freequant?

--Vinay

[vinayakvsv]

If so, then should

  Label-Free Quantification: no                  # precursor label-free quantification inspired by moFF

in the philosopher.yml file be

  Label-Free Quantification: yes                  # precursor label-free quantification inspired by moFF

[huiyinc]

Yes, I think you need to use: freequant: yes # label-free Quantification

Here is an example of philosopher yml file: https://github.com/Nesvilab/philosopher/wiki/Pipeline-mode-for-TMT-analysis

"freequant" is the parameter name used in the example, so I am not sure if Felipe changes "freequant" to "Label-Free Quantitation". Can you tell me where you download (or how you create) the philosopher yml file? Thanks.

Huiyin

[vinayakvsv]

I had tried out the yml file from the wiki, but it was not working in my runs (I later found out that it wasn't running because my annotation.txt file had an extra whitespace at the bottom). I used the yml file included in the repository from Github that I cloned (of version 3.4.13), and Felipe indicates that option as Label-Free Quantitation. I will change it to

  Label-Free Quantification: yes                  # precursor label-free quantification inspired by moFF

and see if this works.

[huiyinc]

Hi Vinay,

Philosopher also allows users to print out the yml file: philosopher pipeline --print

You may find more details at: https://github.com/Nesvilab/philosopher/wiki/Pipeline. Hope this helps.

Huiyin

vinayakvsv @.***> 於 2021年5月30日 週日 下午4:07寫道：

I had tried out the yml file from the wiki, but it was not working in my runs (I later found out that it wasn't running because my annotation.txt file had an extra whitespace at the bottom). I used the yml file included in the repository from Github that I cloned (of version 3.4.13), and Felipe indicates that option as Label-Free Quantitation. I will change it to

Label-Free Quantification: yes # precursor label-free quantification inspired by moFF

and see if this works.

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

[vinayakvsv]

Hello Huiyin,

Philosopher with TMT-integrator successfully ran, and I get non-empty Report_ output tsv files with protein abundances. Thank you for your timely assistance!

--Vinay

[huiyinc]

No problem!

Huiyin

vinayakvsv @.***> 於 2021年5月31日 上午12:16 寫道：

 Hello Huiyin,

Philosopher with TMT-integrator successfully ran, and I get non-empty Report_ output tsv files with protein abundances. Thank you for your timely assistance!

--Vinay

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