Eileen, I see the problem but I don't have a fix for your issue with that CGI program that results from clicking on the protein xpress ratio. There's a process that translates XML data to the resulting web page that you were hoping to see when you click that link. The TPP uses a program xsltproc to transform a pep.xml file to list out the search entries that were quantified for a particular protein. On my linux box, it took its time but ran through fine on your data. On my windows PC, that xsltproc process used up to 2GB of memory and failed with an out of memory error. I don't know if this out of memory error is due to my 32-bit PC being low on memory (it has just 3GB of RAM) or if it hit a 2GB memory cap for 32-bit applications.
At this point, I guess I'd encourage you to simply use ASASPRatio. Or attempt to run the TPP on a 64-bit box and possibly patch c:\inetpub\tpp-bin\xsltproc.exe to access up to 4GB ram (see http://bit.ly/o3fJTo). I don't know if the latter will work or not as I don't use 64-bit Windows here. This belongs in the developers forum but anyone know if there's a good alternative to xsltproc? I was able to manually do the transformation using Xalan and memory usage was much less but it was slow. The underlying pep.xml file being transformed is 338MB which caused xerces to use up to 2GB. On my linux box, xerces consumed 2.1GB when it ran to completion; it failed at just past 2.05GB on Windows. - Jimmy On Thu, Oct 20, 2011 at 2:14 PM, Eileen Yue <y...@ohsu.edu> wrote: > Hi Jimmy: > After I tested one fraction, I run TPP for my 12 fraction together to analyze > the xpress and Asap ratio. They run smoothly and completed after two days. > > There is similar problem like before but without any error information: I > clicked the protein xpress ratio to see the all the peptide xpress ratio > information, they only showed: > > <-- TPP v4.5 RAPTURE rev 0, Build 201109211427 (MinGW) --> > XPressCGIProteinDisplay (TPP v4.5 RAPTURE rev 0, Build 201109211427 (MinGW)) > XPRESS ratio in ProteinProphet: light:heavy (1.29 ± 0.46) > sp|A0AV96|RBM47_HUMAN 6 entries used 1.29:1.00 > 1.00:0.77 > --------------------------------------------------------------------------------c:/Inetpub/wwwroot/ISB/data/ISL1026/isl_er/interact.pep.xml > -------------------------------------------------------------------------------- > Click RELOAD in your browser to re-evaluate ratio if changes have been made > to the XPRESS quantitation in any of the entries above. This will update what > you see in the current ratio just above. > To accept the current ratio back to ProteinProphet, click on the button below. > > > But when I checked the asap ratio, everything is fine. > > Do you know how I solve this problem? > > Thank you > Eileen > > > ________________________________________ > From: spctools-discuss@googlegroups.com [spctools-discuss@googlegroups.com] > On Behalf Of Eileen Yue [y...@ohsu.edu] > Sent: Tuesday, October 18, 2011 3:22 PM > To: spctools-discuss@googlegroups.com > Subject: RE: [spctools-discuss] ASAP Ratiopeptideparse.exe-application error > > Hi Jimmy: > Thank you so much and it works! I just tried one fraction and it works > perfectly! > > So appreciate all of you for your kind help! > > Eileen > ________________________________________ > From: spctools-discuss@googlegroups.com [spctools-discuss@googlegroups.com] > On Behalf Of Jimmy Eng [jke...@gmail.com] > Sent: Tuesday, October 18, 2011 1:41 PM > To: spctools-discuss@googlegroups.com > Subject: Re: [spctools-discuss] ASAP Ratiopeptideparse.exe-application error > > Eileen, > > Can you download the following executable and update your TPP binary > with this one: > > http://proteomicsresource.washington.edu/dist/XPressPeptideUpdateParser.cgi > > The files should go in c:\inetpub\tpp-bin\. Let me know if this fix > does not work for the problem you're experiencing. > > - Jimmy > > On Tue, Oct 18, 2011 at 10:51 AM, Eileen Yue <y...@ohsu.edu> wrote: >> Hi Joe: >> I did convert mzml files. the problem is that the error showed up when I >> click the xpress ratio in prot.xml files. If I open the pep.shtml and click >> the xpress ratio, it is fine and showed me the chromatrography information >> for this peptide. This will not work if I open the prot.shtml and click the >> xpress ratio. The ASAP ratio is fine and I can open them and see the >> chromatography information. >> >> Thanks >> Eileen > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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