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 > 在 2017年11月17日，22:47，David Shteynberg <david.shteynb...@systemsbiology.org> 写道： > > 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 > >> On Fri, Nov 17, 2017 at 12:46 AM, Elkan Dong <np.dong...@gmail.com> wrote: >> 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： >>> >>> 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 >>> >>>> On Mon, Jun 19, 2017 at 9:46 AM, Ada A <ada.an...@gmail.com> wrote: >>>> 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 >>>> -- >>>> You received this message because you are subscribed to the Google Groups >>>> "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send an >>>> email to spctools-discu...@googlegroups.com. >>>> To post to this group, send email to spctools...@googlegroups.com. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to spctools-discuss+unsubscr...@googlegroups.com. >> To post to this group, send email to spctools-discuss@googlegroups.com. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
