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 <jke...@gmail.com> 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
> <quandt.andr...@gmail.com> 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 <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
>>>>> >
>>>>> > --
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