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Q-Exactive files can not pass through labkey CPAS

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Q-Exactive files can not pass through labkey CPAS dwang7  2013-05-15 09:31
Status: Closed
 
Hi there,
I have a very strange problem. I have 12 Q-exactive raw data; I converted using two versions of msconvert (pwiz version 3.0.3398, which is shipped with labkey 13.1), msconvert (pwiz version 3.0.4472, which I download myself). Here is my testing:
1. msconvert (old) --mzXML --zlib: can not be completed. Error message:
processing file: IPAS_0512_HCD_TCE_SG78to84.raw
[ThermoRawFile] [RawFile::ctor] Unable to initialize XRawfile; is MSFileReader installed? Reading Thermo RAW files requires MSFileReader to be installed. It is available for download at:
http://sjsupport.thermofinnigan.com/public/detail.asp?id=703
Error processing file IPAS_0512_HCD_TCE_SG78to84.raw

2. msconvert (new) --mzXML --zlib: can not be recognized by labkey xtandem (2009 version)
3. msconvert (new) --mzXML: can not be recognized by labkey xtandem (2009 version)
4. msconvert (new) --mzXML --zlib: can not be recognized by xtandem (2013 version, zlib not recognized)
5. msconvert (new) --mzXML --zlib: successfully recognized by xtandem (2013 version)

The error log file on which the xtandem (2009 version) failed were attached below.

Can anyone here give me hits of how to deal with Q-E data with our current labkey CPAS 13.1? I tried to replace it with xtandem 2013, but this does not support k_score. In my previous communication with labkey support, they said they used 2009 version because this is what TPP has; but I checked with TPP, their current release version is 4.6.2, which contains 2011 version of xandem. Question is: how this will affect the future release of labkey?

Any efforts to solve my Q-Exactive searches will be greatly appreciated. Thanks.

Best,
Dong Wang
 
 
jeckels responded:  2013-05-17 15:01
Hello,

As you've seen, the k_score algorithm is available in the TPP-based XTandem distribution, but is not included in the core XTandem build from thegpm.org.

Have you tried running the latest TPP XTandem binary to see if it works with your mzXML file?

In a future release, we will incorporate a newer build of the TPP, but it isn't a high priority issue for any of our current customers so it's not currently scheduled. We have not yet tested with the newer versions, which in some cases work just fine as a drop-in replacement, and in other cases introduce incompatibilities that require code changes to LabKey Server to work properly.

You can certainly grab the current TPP, including XTandem, and try using it instead of the version included in the LabKey Server distribution. It may just work.

Thanks,
Josh