Analyze peptides- error

[Ada A]

Hello,

I was trying to run peptide analysis with PeptideProphet but it keeps showig me error...
I was using dimethyl labeling technique and peptides were identified using Mascot. I exported all data from Mascot, uploaded here and it fails to do anything. I was wondering whether anyone could advice me what should I do with it? I would be grateful for some help.

Here is what it shows me:

C:/TPP/bin/xinteract (TPP v5.0.0 Typhoon, Build 201610111222-7423 (Windows_NT-x86_64))
 PPM mode in Accurate Mass Model ...
C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a09964\': File exists

command "C:\TPP\bin\mkdir.exe -p "/tmp/a09964/"" failed: Operation not permitted
could not create temp dir /tmp/a09964/, working in data directory

running: "C:/TPP/bin/InteractParser "interact.pep.xml" "H7(3).pep.xml" "h7(3).xml" -L"7""
 file 1: H7(3).pep.xml
WARNING: empty raw_data in msms_run_summary tag ... trying mzML ...
Failed to open input file 'c:/TPP/data/.mzML'.
WARNING: cannot open data file c:/TPP/data/.mzML in msms_run_summary tag ...... trying .mzXML ...
Failed to open input file 'c:/TPP/data/.mzXML'.
WARNING: cannot CORRECT data file c:/TPP/data/.mzXML in msms_run_summary tag ...
WARNING: empty raw_data in msms_run_summary tag ... trying mzML ...
Failed to open input file 'c:/TPP/data/.mzML'.
WARNING: cannot open data file c:/TPP/data/.mzML in msms_run_summary tag ...... trying .mzXML ...
Failed to open input file 'c:/TPP/data/.mzXML'.
WARNING: cannot CORRECT data file c:/TPP/data/.mzXML in msms_run_summary tag ...

Kind Regards,

Ada

[David Shteynberg]

Hello Ada,

One immediate problem I notice is that your files contain parenthesis character.  Please name your files using only alphanumeric and underscore character, please no special characters or whitespace.  Also, you might consider using comet search engine, support for which is more streamlined in the TPP.

Cheers,

-David

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[Elkan Dong]

I'm using the newest version of TPP, but encountered the same error when using PeptideProphet. The file name I used looks like 

I08-F4-SAX1.pep.xml

Any solution?

Thanks.

Elkan


在 2017年6月20日星期二 UTC+8上午1:28:34，David Shteynberg写道：

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[David Shteynberg]

Hello Elkan,

Although unlikely, the dashes in your filename could be the issue.  In my email on this thread I mentioned that only alphanumerics and underscores "_" should be utilized.  If that fails there is a problem with the pep.xml file itself, that you would need to troubleshoot.  How was the file generated? 

-David   

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[np.do...@gmail.com]

Hi David,

All the xml files are generated by Comet search in command line. Ok, I will revise the file names to meet the requirements and run PeptideProphet again. Wish everything go right.

Thanks.

Regards,

Elkan

发自我的 iPad

[Elkan Dong]

Hi David,

Still encountered the problem.

C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 (Windows_NT-x86_64))

 PPM mode in Accurate Mass Model ...

C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a04316\': File exists

command "C:\TPP\bin\mkdir.exe -p "/tmp/a04316/"" failed: Operation not permitted
could not create temp dir /tmp/a04316/, working in data directory

running: "C:/TPP/bin/InteractParser "interact.pep.xml" "I17F1SAX.decoy.pep.xml" "I17F1SAX.pep.xml" "I17F1SCX.decoy.pep.xml" "I17F1SCX.pep.xml" "I17F2SAX.decoy.pep.xml" "I17F2SAX.pep.xml" "I17F2SCX.decoy.pep.xml" "I17F2SCX.pep.xml" "I17F3SAX.decoy.pep.xml" "I17F3SAX.pep.xml" "I17F3SCX.decoy.pep.xml" "I17F3SCX.pep.xml" "I17F4SAX.decoy.pep.xml" "I17F4SAX.pep.xml" "I17F4SCX.decoy.pep.xml" "I17F4SCX.pep.xml" "I17F5SAX.decoy.pep.xml" "I17F5SAX.pep.xml" "I17F5SCX.decoy.pep.xml" "I17F5SCX.pep.xml" "I17F6SAX.decoy.pep.xml" "I17F6SAX.pep.xml" "I17F6SCX.decoy.pep.xml" "I17F6SCX.pep.xml" "I17F7SAX.decoy.pep.xml" "I17F7SAX.pep.xml" "I17F7SCX.decoy.pep.xml" "I17F7SCX.pep.xml" "I17F8SAX.decoy.pep.xml" "I17F8SAX.pep.xml" "I17F8SCX.decoy.pep.xml" "I17F8SCX.pep.xml" -L"5""

Regards,

Elkan

在 2017年11月17日星期五 UTC+8下午10:47:29，David Shteynberg写道：

[David Shteynberg]

Looks like this is not an error message but some information.  It seems that the process actually got past this point.  Are you certain that the command dies here?  Can you see the output file interact.pep.xml in your working directory?  You can try deleting the directory C: /tmp/a04316/ to seeing this particular message.

-David

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[Darya Laptanovich]

Hello David!

I have the same problem. After running the command I've got this info message:

C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 (Windows_NT-x86_64))
 PPM mode in Accurate Mass Model ...
C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a04048\': File exists

command "C:\TPP\bin\mkdir.exe -p "/tmp/a04048/"" failed: Operation not permitted
could not create temp dir /tmp/a04048/, working in data directory

running: "C:/TPP/bin/InteractParser "interact.pep.xml" "search.pep.xml" -L"7"" 

And after this there is new file interact.pep.xml.tmp.a04100 created in directory C:\tmp\a05484 while my data directory is C:\TPP\data

 

понедельник, 20 ноября 2017 г., 8:38:59 UTC+3 пользователь David Shteynberg написал: