Re: [proteowizard-support] peakaboo in CPAS error

[TOMAS V. <tvaisar@u.washington.edu>]

Hi Darren,

Thanks a lot for getting back to me. I could probably cut the first few lines of the mzXML file and send it to you.  Would that work?  Whole file is >300 MB.

Tomas

On Tue, 4 Nov 2008, Darren Kessner wrote:

> Hi Tomas,
>
> There is probably something weird about the encoding of the instrument type in 
> your mzxml file.
> Could you put it somewhere where I can take a look at it?
>
> Thanks,
>
> Darren
>
>
> On Mon, 3 Nov 2008 11:15 am, Tomas Vaisar wrote:
>> Hello,
>> 
>> I have tried to run the peakaboo in the new release of the CPAS (8.3)
>> and ran into the following problem:
>> 
>> I tried to run peakaboo on a mzXML file from Orbitrap, but got following
>> error:
>> 
>> 30 Oct 2008 18:01:51,232 INFO : peakaboo output
>> 30 Oct 2008 18:01:51,232 INFO : =======================================
>> 30 Oct 2008 18:01:51,233 INFO : Working directory is
>> /data/heinecke_lab/pipe/Proteomics/users/Tomas_Vaisar/peakaboo0810A/inspect/CPAS83MS1_test4/080731APHDLAg1_02.work
>> 
>> 30 Oct 2008 18:01:51,234 INFO : running: /usr/local/labkey/bin/peakaboo
>> --e .peaks.xml ../../../080731APHDLAg1_02.mzXML
>> 30 Oct 2008 18:01:51,261 INFO : outputPath: .
>> 30 Oct 2008 18:01:51,264 INFO : extension: .peaks.xml
>> 30 Oct 2008 18:01:51,265 INFO :
>> 30 Oct 2008 18:01:51,266 INFO : Processing file:
>> ../../../080731APHDLAg1_02.mzXML
>> 30 Oct 2008 18:01:51,266 INFO : outputFilename:
>> ./080731APHDLAg1_02.peaks.xml
>> 30 Oct 2008 18:01:51,924 INFO : scans: 32457
>> 30 Oct 2008 18:01:51,925 INFO : Using Orbitrap settings.
>> 30 Oct 2008 18:01:52,335 INFO : Skipping non-FT scan 1
>> 30 Oct 2008 18:01:52,340 INFO : Skipping non-FT scan 2
>> 30 Oct 2008 18:01:52,341 INFO : Skipping non-FT scan 3
>> 30 Oct 2008 18:01:52,341 INFO : Skipping non-FT scan 4
>> 30 Oct 2008 18:01:52,342 INFO : Skipping non-FT scan 5
>> 30 Oct 2008 18:01:52,343 INFO : Skipping non-FT scan 6
>> 30 Oct 2008 18:01:52,344 INFO : Skipping non-FT scan 7
>> 30 Oct 2008 18:01:52,344 INFO : Skipping non-FT scan 8
>> 30 Oct 2008 18:01:52,345 INFO : Skipping non-FT scan 9
>> 30 Oct 2008 18:01:52,346 INFO : Skipping non-FT scan 10
>> 30 Oct 2008 18:01:52,346 INFO : Skipping non-FT scan 11
>> 30 Oct 2008 18:01:52,347 INFO : Skipping non-FT scan 12
>> and that goes on through all the 32000 scans
>> 
>> The MSInspect finds features after that and provides a list of features
>> so the run does not fail and the MS1 page shows the peakaboo option
>> [details].
>> The data was acquired in the profile mode for MS and centroided for MSMS.
>> 
>> Would you have any suggestions what could be wrong with the mzXML file
>> that the data is not recognized correctly?
>> 
>> Thanks a lot.
>> 
>> Tomas Vaisar
>> 
>> +++++++++++++++++++
>> 
>> Tomas Vaisar, Ph.D.
>> Research Assistant Professor
>> Director, Proteomics Core
>> Department of Medicine
>> N222, Box 358055
>> University of Washington
>> 815 Mercer St
>> Seattle, WA 98109
>> 
>> Phone: 206-616 4972
>> FAX: 206-543-3567
>> 
>> 
>> 
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>
> Darren
>