Re: [proteowizard-support] [spctools-discuss] how to convert Agilent ETD trap data to XML?

[Natalie T. <nat...@in...>]

Hello Zeyu,

You're using the TPP's "trapper" program.  Trapper is designed for data 
from Agilent's *MassHunter* program.  This data is stored in a .d 
folder.  However, there is a confusing situation: two different Agilent 
formats use .d folders.  Your .d folder has the different format: 
analysis.yep.  I'm guessing that you're probably using data acquired 
with Agilent's *ChemStation* program.  Trapper does not handle .yep.  
But, msconvert, which is included with the TPP and comes from the 
ProteoWizard (pwiz) project, might handle this type of data.  I'm 
forwarding this message to the pwiz discussion list as well, and 
hopefully they can suggest a way to proceed.

There is an

-Natalie


On 2/10/10 11:16 PM, zeyu sun wrote:
> Hi, I have a problem to convert the .d folder from a ETD trap to xml format. I have no problem to convert .d folderto xml for spectrum from Q-tof. Here is what I saw in the commend line:
>
> Settings:
>    centroid scans: 0
>
>    compress scans: 0
>    verbose mode: 1
>    skip checksum: 0
>    deisotope:0
>    requirePeptideLikeAbundanceProfile: 0
>    relativeTolerance: 0
>    absoluteTolerance: 0
>    limitChargeState:0
>    maxChargeState: 0
>
>    mzML mode: 0
>    mzXML mode: 1
>    input filename: c:/Inetpub/wwwroot/ISB/data/ZSMOAC.D
>    output filename: c:/Inetpub/wwwroot/ISB/data/ZSMOAC.mzXML
>
> ERROR at .\MHDACWrapper.cpp, 60:
> HR = -2147024894
> OpenDataFile
>
> unable to open c:/Inetpub/wwwroot/ISB/data/ZSMOAC.D with MassHunter interface
>    
> *Command FAILED*
>
>
> by the way, the .d folder comprised of a analysis.yep file (very big, 
> which I assume is where the MS data stored), a LCDIAG.reg file, a 
> extension.baf file, a sample.mac file, 3 txt files named 
> LCMETHODAUDITTRAIL, lcparms, RUN, and a folder ETD_LONGCHIP_100128.M.
>
> Any thought how to do the conversion?
> Thank you very much!
>
>
> -- 
> Zeyu Sun
>
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