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-discuss@googlegroups.com [spctools-discuss@googlegroups.com] On Behalf Of Jimmy Eng [jke...@gmail.com] Sent: Thursday, May 02, 2013 9:16 AM To: spctools-discuss@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 <y...@ohsu.edu<mailto:y...@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 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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