The problem is due to starting out with the mgf file. Libra and the TPP tools needs to know which spectrum/scan in the mgf/mzML file is associated with which identification. So there needs to be some type of convention in how the mgf file annotates this which means you can't start with just any mgf file. That mgf file needs to be produced by the TPP tools or with msconvert such that the TITLE line for each spectrum is of the format:
TITLE=<basename>.<scan>.<scan>.<charge> e.g. TITLE=JE102306.00594.00594.2 If you have your mgf in this file, tools such as Comet will/should annotate that scan as scan 594 in the "spectrum_query" element of the pep.xml file. Libra will then know to read scan 594 of the corresponding mzML/mzXML file to pull out the iTRAQ/TMT peaks. Again, if you start out with an mzML file, you can generate the mgf using the TPP tools and it will have the correct format. You can also start out with a raw file or mzML and use msconvert with the following titleMaker option to accomplish the same thing: --filter "titleMaker <RunId>.<ScanNumber>.<ScanNumber>.<ChargeState> There's no easy fix that I'm aware of if you start with a random mgf file that does not have TITLE lines that conform to this convention. - Jimmy On Wed, Oct 28, 2015 at 5:13 PM, zeyu sun <szy3...@gmail.com> wrote: > Hi, Henry, > I have the same problem. I use the the Comet to do the search, and when I > use Libra function in peptide analysis module, I got this message: > > Error ms2 filter line: > > I don't really know what causes this, anyone in TPP team know how to solve > this? > > > SunSun > > > > On Sunday, March 29, 2015 at 8:10:34 AM UTC+8, Henry RodrÃguez wrote: >> >> Hi, >> >> I am performing a quantification of my data with Libra software. However, >> I always obtain a error. My original spectra are in *MGF format*, so I >> convert them to mzML with MSConvert software of Proteowizard with different >> filters, but this does not functioned. Also, I have tried use the >> ScanRanker software which filter for quality the spectra ( >> http://fenchurch.mc.vanderbilt.edu/bumbershoot/scanranker/index.html), >> but this also does not functioned. The error that I have obtained is the >> following. Thanks for your help with this error, >> >> Henry. >> >> >> >> Analyzing interact_rawdata280315.pep.xml ... >> Parsing search results >> "c:/Inetpub/wwwroot/ISB/data/Rawdata_Peakpicking2/PAIV141024_1 (X! Tandem >> (k-score))"... >> => Found 34 hits. (0 decoys, 0 excluded) >> => Total so far: 34 hits. (0 decoys, 0 excluded) >> Parsing search results >> "c:/Inetpub/wwwroot/ISB/data/Rawdata_Peakpicking2/PAIV141024_2 (X! Tandem >> (k-score))"... >> => Found 68 hits. (0 decoys, 0 excluded) >> => Total so far: 102 hits. (0 decoys, 0 excluded) >> El sistema no puede encontrar la ruta especificada. >> command completed in 1 sec >> >> running: "C:/Inetpub/tpp-bin/LibraPeptideParser >> "interact_rawdata280315.pep.xml" -ccondition.xml" >> Error ms2 filter line: >> >> >> command "C:/Inetpub/tpp-bin/LibraPeptideParser >> "interact_rawdata280315.pep.xml" -ccondition.xml" failed: Operation not >> permitted >> >> command "C:/Inetpub/tpp-bin/LibraPeptideParser >> "interact_rawdata280315.pep.xml" -ccondition.xml" exited with non-zero exit >> code: 1 >> QUIT - the job is incomplete >> >> -- > 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 http://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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
