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-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.
