hey brian, nice to hear from you too and also thanks for picking up on this :-) according to xmlwf the modified.mzXML is valid. i uploaded both, original.mzXML and modified.mzXML to ftp.systemsbiology.net/incoming. it would be great if you guys could spare some time to help me with this as i am completely clueless about what i am doing wrong.
cheers, andreas On Tue, Mar 23, 2010 at 9:25 PM, Brian Pratt <brian.pr...@insilicos.com>wrote: > Does the file pass general XML validation? That is, did you possibly > damage it structurally? > > It's hard to discuss these things without looking at the actual file, can > you upload to the group's files area? > > Brian > > On Tue, Mar 23, 2010 at 1:20 PM, Andreas Quandt > <quandt.andr...@gmail.com>wrote: > >> hey luis, >> >> nice to hear from you and many thanks for your fast answer! >> unfortunately this does not do the trick :-( >> >> i renumbered the scans starting from 1 (for ms1 and ms2 in ascending >> order), >> ran indexmzXML on the file (successfully) and >> tried 'MzXML2Search -mgf' afterwards. >> and then MzXML2Search fails with an segmentation fault: >> >> $ /usr/local/apps/tpp/bin/MzXML2Search -mgf modified.mzXML >> >> output mode selected: Mascot Generic Format >> MzXML2Search - Mascot Generic Format >> >> Reading modified.mzXML >> Getting the index offset >> Reading the index >> scan: 34 000%Segmentation fault >> >> Do you have any further ideas? >> >> cheers, >> andreas >> >> >> >> >> >> >> On Tue, Mar 23, 2010 at 5:49 PM, Luis Mendoza < >> lmend...@systemsbiology.org> wrote: >> >>> Hi Andreas, >>> You may need to re-number the indices so that the scans start at 1 >>> have no gaps between subsequent ones, as well as adjust the total scan >>> count in the header of the file. Then apply the re-indexing. >>> >>> Hope this helps, >>> --Luis >>> >>> >>> >>> On Tue, Mar 23, 2010 at 9:46 AM, Andreas Quandt >>> <quandt.andr...@gmail.com> wrote: >>> > dear list, >>> > >>> > i modified some of my mzXML files by removing ms2 spectra which did not >>> > fulfill certain criteria. >>> > afterwards i tried to analyze them via xtandem but got error messages >>> like >>> > "might be a corrupted file". >>> > to overcome this problem i used indexmzXML which corrected the index by >>> > generating a new mzXML file. >>> > unfortunately this did not solve the problem as neither xtandem nor >>> > mzxml2search where accepting the modified mzXML files as correct input. >>> > >>> > hence, i was wondering if there is either a better way to remove my ms2 >>> > scans from the file or if i am using indexmzXML not in a proper way? >>> > >>> > cheers, >>> > andreas >>> > >>> > -- >>> > 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<spctools-discuss%2bunsubscr...@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-disc...@googlegroups.com. >>> To unsubscribe from this group, send email to >>> spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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-disc...@googlegroups.com. >> To unsubscribe from this group, send email to >> spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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-disc...@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.
