Re: [spctools-discuss] Installing TPP 4.6.2 on Mountain Lion

[Luis Mendoza]

Thank you, Bosco!

I have added a link to your page from our wiki:

http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP#Mac_OSX

--Luis

On Mon, Apr 22, 2013 at 6:22 PM, Bosco Ho <appo...@gmail.com> wrote:

If anyone is interested, I figured it out:

http://boscoh.com/protein/installing-the-tpp-462-on-mountain-lion-mac-osx

Bosco. Monash Proteomics Facility.Bosco

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[Eileen Yue]

Hello everyone.
I have one error information when I tried to analyze peptide for SILAC data. I do not know whether this is possibly caused by file's name which includes "+" and "-" . I did manually change the pep.xml and mzml files's name (which I deleted "+" and "-" ) but I still get error information. Could anyone give me some advice about this issue?

Thanks
Eileen



XPRESS error - cannot open file from basename c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2, will try to derive from scan names

command "C:/Inetpub/tpp-bin/XPressPeptideParser "interact.pep.xml" -m1 -nK,8 -nR,10 -c6 -p1" failed: Unknown error

command "C:/Inetpub/tpp-bin/XPressPeptideParser "interact.pep.xml" -m1 -nK,8 -nR,10 -c6 -p1" exited with non-zero exit code: -1073741819
QUIT - the job is incomplete

command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.75 -l6 -Op -dREV -X-m1-nK,8-nR,10-c6-p1 -A-lKR-r0.5 MAY1335_Yeast_1+4-D_100ug_IMAC_75um_140_20130410_VE2.pep.xml MAY1335_Yeast_1+4-D_100ug_POLY-Ti_75um_140_20130410_VE2.pep.xml MAY1335_Yeast_1+4-D_100ug_PierceIMAC_75um_140_20130423_VE2.pep.xml MAY1335_Yeast_2+3-D_100ug_IMAC_75um_140_20130410_VE2.pep.xml MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.pep.xml MAY1335_Yeast_2+3-D_100ug_POLY-Ti_75um_140_20130410_VE2.pep.xml" failed: Unknown error

Command FAILED

[Jimmy Eng]

Eileen,

The "+" in the file names is not a problem at this stage of processing although it is a reserved character for a URL so you will have issues visualizing results in the web interface.  The "-" character is OK.  For future reference, it's not enough to simply change the pep.xml and mzML file names.  You will have to also make the corresponding changes to the content within the pep.xml file, specifically the "base_name" attributes.  I always suggest that researchers stick to numbers, letters, dash "-", and underscore "_" in naming files.

For your specific error, does the following file exist?

 c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.mzML

If yes, I couldn't tell you why XPRESS is reporting that error.  I would suggest you try this analysis with just a single input file first to confirm you can run the tools to completion.  If that works, try this processing this one MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.mzML file by itself.

- Jimmy

[Eileen Yue]

Hi Jimmy,
thank you for your advice. I followed your advice and test the files one by one and figured out one raw file name is different from the sequest search file name (my colleague renamed the sequest search result file name). After I renamed the raw file name to match the sequest results name. then the analyze peptide went through without any problem.

The new problem is: when I click the peptide to check the xpress ratio infomration or ms/ms informatin, there is error information showed below. Could you give me some advice for this error information?

Thank you so much and have a nice weekend
Eileen
________________________________________
for ms/ms information erro:

command "c:\Inetpub\wwwroot\..\tpp-bin\tar.exe -tzf c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_1 4-D_100ug_PierceIMAC_75um_140_20130423_VE2.tgz "*MAY1335_Yeast_1 4-D_100ug_PierceIMAC_75um_140_20130423_VE2.22310.22310.3.dta" > /dev/null" failed: Operation not permitted Error - cannot read spectrum; tried direct .dta, from mzXML/mzData and from .tgz


for xpress information error:

Light scans: mass: tol:
Heavy scans: mass: Z:

Raw file:
.out file: Norm:

Error - cannot open file "c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_1".



----------------------------------------------------------------------------------------------------------------------------------------

From: spctools...@googlegroups.com [spctools...@googlegroups.com] On Behalf Of Jimmy Eng [jke...@gmail.com]
Sent: Thursday, May 02, 2013 9:16 AM
To: spctools...@googlegroups.com
Subject: Re: [spctools-discuss] why I got this error information?

Eileen,

The "+" in the file names is not a problem at this stage of processing although it is a reserved character for a URL so you will have issues visualizing results in the web interface. The "-" character is OK. For future reference, it's not enough to simply change the pep.xml and mzML file names. You will have to also make the corresponding changes to the content within the pep.xml file, specifically the "base_name" attributes. I always suggest that researchers stick to numbers, letters, dash "-", and underscore "_" in naming files.

For your specific error, does the following file exist?
c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.mzML
If yes, I couldn't tell you why XPRESS is reporting that error. I would suggest you try this analysis with just a single input file first to confirm you can run the tools to completion. If that works, try this processing this one MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.mzML file by itself.

- Jimmy

On Wed, May 1, 2013 at 1:27 PM, Eileen Yue <yu...@ohsu.edu<mailto:yu...@ohsu.edu>> wrote:

Hello everyone.
I have one error information when I tried to analyze peptide for SILAC data. I do not know whether this is possibly caused by file's name which includes "+" and "-" . I did manually change the pep.xml and mzml files's name (which I deleted "+" and "-" ) but I still get error information. Could anyone give me some advice about this issue?

Thanks
Eileen



XPRESS error - cannot open file from basename c:/Inetpub/wwwroot/ISB/data/MAY1335_Phosphopeptides/MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2, will try to derive from scan names

command "C:/Inetpub/tpp-bin/XPressPeptideParser "interact.pep.xml" -m1 -nK,8 -nR,10 -c6 -p1" failed: Unknown error

command "C:/Inetpub/tpp-bin/XPressPeptideParser "interact.pep.xml" -m1 -nK,8 -nR,10 -c6 -p1" exited with non-zero exit code: -1073741819
QUIT - the job is incomplete

command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.75 -l6 -Op -dREV -X-m1-nK,8-nR,10-c6-p1 -A-lKR-r0.5 MAY1335_Yeast_1+4-D_100ug_IMAC_75um_140_20130410_VE2.pep.xml MAY1335_Yeast_1+4-D_100ug_POLY-Ti_75um_140_20130410_VE2.pep.xml MAY1335_Yeast_1+4-D_100ug_PierceIMAC_75um_140_20130423_VE2.pep.xml MAY1335_Yeast_2+3-D_100ug_IMAC_75um_140_20130410_VE2.pep.xml MAY1335_Yeast_2+3-D_100ug_PIMAC_75um_140_20130423_VE2.pep.xml MAY1335_Yeast_2+3-D_100ug_POLY-Ti_75um_140_20130410_VE2.pep.xml" failed: Unknown error

Command FAILED


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[Jimmy Eng]

Eileen,

Any chance you have a "+" in your file name?  If yes, that is your problem.  And based on your error message you pasted, this looks like the case.  If you re-named your pep.xml and mzML files, you will also have to change all references *inside* the pep.xml file to the updated name which I mentioned in my previous reply.

To avoid all these issues with mis-naming files and not correctly updating file names & content inside the pep.xml files, consider starting from the beginning with a re-named mzML file, do the search to generate a pep.xml file and then run the TPP tools. 

- Jimmy

[Eileen Yue]

Jimmy,

You are right. I do have “+” in my file name.  I need rename the raw file name and redo the Sequest search  first, then I will load on TPP to switch to MZML and pep. Xml file.

 

Thank you so much for your kind help

Eileen