Andreas, I don't believe Brian or any other helpful external person can access the files when you place it in ISB's ftp site.
Anyways, the ramp parser is frail and finicky and expects an mzXML to be formatted just the way it expects. Your modified mzXML has a lot of formatting changes. The biggest difference I notice is the base64 encoded peak list normally begins right after the closing "<peaks ...>" tag but your new file has a newline and whitespace between the closing '>' and before the base64 starts. I can see why MzXML2Search might die because of this change but interestingly readmzXML, which uses same ramp parser, seems fine. I'm spending a little time on this just 'cause I find it interesting ... maybe the files can be posted to a more accessible area if others wish to look too. - Jimmy On Tue, Mar 23, 2010 at 1:57 PM, Andreas Quandt <[email protected]> wrote: > 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 <[email protected]> > 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 <[email protected]> >> 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 >>> <[email protected]> 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 >>>> <[email protected]> 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 >>>> > [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. >>>> >>> >>> -- >>> 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. > > -- > 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. 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