Hey Jimmy, hello Brian, Many thanks for your help! Jimmy was right, problem was tha I used an XML parser which 'prettyfied' the file. By changing to a text parser everthung worked out properly. Also by using a text parser, it is not any longer necessary to use the indexmzxml program any longer.
Cheers Andreas On Mar 23, 2010, at 10:55 PM, Jimmy Eng <[email protected]> wrote: > Andreas, > > When I modified your file get rid of all whitespace between the > <peaks> tags, the MzXML2Search program subsequently ran fine. > > change: > <peaks precision="32" byteOrder="network" pairOrder="m/z-int"> > Q0BLmUBez4BDSRBhQQDRN0NN...w== > </peaks> > > to: > <peaks precision="32" byteOrder="network" > pairOrder="m/z-int">Q0BLmUBez4BDSRBhQQDRN0NN...w==</peaks> > > and then re-index. > > > On Tue, Mar 23, 2010 at 2:29 PM, Jimmy Eng <[email protected]> wrote: >> 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. > To post to this group, send email to spctools- > [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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