Hi Thomas,
Thank you for the patch! I just committed it to the SVN.
It will be included in MZmine 2.3, which should be out in a few weeks.
Best regards,
Tomas
On Jun 14, 2011, at 12:41 AM, Thomas McGrew wrote:
> Tomas & Lindsay,
>
> MzXMLReadTask is assuming a precision of 32 bits for some reason. This file
> has 64 bit precision and so the data is being garbled by the import. I have
> attached a patch which should remedy this problem. The mzdata and MzML
> readers appear to check the precision value properly.
>
> Thomas McGrew
> Data Analyst/Programmer
> Bindley Bioscience Center @ Purdue University
>
>
>
> On Sun, Jun 12, 2011 at 9:55 PM, Lindsay Edwards <l.m.edwa...@utas.edu.au>
> wrote:
> Hi Tomas,
>
> Here's one:
>
> http://dl.dropbox.com/u/1998606/7053.mzXML.mzxml
>
> The file was generated using Thermo Xcalibur.
>
> L.
>
> _________
>
>
>
> Dr Lindsay Edwards MSc DPhil (Oxon) MSB
> ____________________________________________
> Lecturer and Theme 5 Coordinator | University of Tasmania School of Medicine
> Honorary Member and Fellow | Menzies Research Institute
> Visiting Researcher | University of Oxford
> Private Bag 34, Medical Sciences 1, Hobart 7001, TAS
> Ph: +61 (3) 6226 2677 Email: l.m.edwa...@utas.edu.au
> PubMed - "Edwards L AND (Clarke K OR Jobson S)"
> _____________________________________________
>
> On 13/06/2011, at 10:15 AM, Tomas Pluskal wrote:
>
>> Hi Lindsay,
>>
>> Can you please send an example of such mzXML file?
>> What software did you use to produce the mzXML?
>>
>> Best regards,
>>
>> Tomas
>>
>> On Jun 12, 2011, at 5:43 AM, Lindsay Edwards wrote:
>>
>>> I am trying to analyse data from our Orbitrap using mzMine.
>>>
>>> When loading mzXML files, it looks as thought the m/z and intensity data
>>> have got scrambled (screenshot attached).
>>>
>>> FYI, the data is centroided. Any ideas how to get round this?
>>>
>>> In the meantime I am going to load RAW files using mzMine running on
>>> Virtual Box.
>>>
>>> Thanks for your help,
>>>
>>> Lindsay.
>>>
>>>
>>> --
>>> Dr Lindsay Edwards MSc DPhil (Oxon) MSB
>>> Lecturer in Biomedical Science, School of Medicine
>>> University of Tasmania
>>> Visiting Researcher, University of Oxford
>>> Email: l.m.edwa...@utas.edu.au
>>> Ph: +61 (3) 6226 2677
>>> Mail: Private Bag 34, Medical Sciences 1
>>> Hobart 7000, Tasmania
>>> PubMed - "Edwards L AND (Clarke K OR Jobson S)"
>>>
>>> <Screen shot 2011-06-12 at 6.42.24 AM.png>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> EditLive Enterprise is the world's most technically advanced content
>>> authoring tool. Experience the power of Track Changes, Inline Image
>>> Editing and ensure content is compliant with Accessibility Checking.
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>>> Mzmine-devel@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>>
>> ===============================================
>> Tomas Pluskal
>> G0 Cell Unit, Okinawa Institute of Science and Technology
>> 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
>> TEL: +81-98-966-8684
>>
>>
>>
>>
>
>
> ------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> _______________________________________________
> Mzmine-devel mailing list
> Mzmine-devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>
>
> <mzmine_mzxml_fix.patch>------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
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===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology
1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
TEL: +81-98-966-8684
------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
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