I wrote a java program that can parse the pepxml files of tpp into a tab delimited file. dfermin.com/software/
Look for tppXMLparser.jar On Feb 14, 5:49 pm, Kinfai Au <[email protected]> wrote: > Thank you! > I tried to use pepxml viewer browser on TPP interface. I enter the > following > URL:http://localhost/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/wwwr... > > However, I got the error message on the browser as: > > could not delete /tmp/PepXMLViewera09972, error 13 "Permission denied" > error: *unable to read pepxml file: error parsing pepxml file: XML parsing > error: junk after document element, at xml file line 1326525, column 0* > > I checked the line *1326525 of the file, it is: > > *<msms_run_summary > base_name="/home/kinfai/PROTOMAP/sHEK_xtandem/4/022111_HEK_media_band4" > search_engine="X! Tandem (k-score)" msManufacturer="Thermo Scientific" > msModel="LTQ" msIonization="nanoelectrospray" msMassAnalyzer="radial > ejection linear ion trap" msDetector="electron multiplier" > raw_data_type="raw" raw_data=".mzML"> > > I don't know what is wrong.... do you have any clues? > btw, I ran my Xtandem in linux system. > > > > > > > > On Mon, Feb 13, 2012 at 5:22 AM, 永远地流浪 <[email protected]> wrote: > > Go to Utilities\Browse Files or any other command that can browse > > peptideprophet output file .pep.xml, then you can see a link as [PepXML] > > that can view the output file. Click the link and view .pep.xml file in new > > window. On the head line, click "Other Actions", then you will see a botton > > named Export Spreadsheet. Click the botton, an excel file would then > > generated with same name as the .pep.xml file. > > > ------------------ Original ------------------ > > *From:* "Kinfai Au"**; > > *Date:* 2012年2月13日(星期一) 晚上9:11 > > *To:* "spctools-discuss"**; > > *Subject:* [spctools-discuss] [peptideprophet] tab-delimited output? > > > I have a small problem for TPP. After peptideprophet, how can I > > convert the peptide identification results to a tab-delimited file or > > excel file? > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to > > spctools-dis**cuss@googleg**roups.com<[email protected]> > > . > > To unsubscribe from this group, send email to spctools-discuss+ > > unsubscribe@**googlegroups**.com <[email protected]>. > > For more options, visit this group athttp://group**s.google.com** > > /group/spcto**ols-discuss?**hl=en.<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 [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > 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 [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
