how to convert Agilent ETD trap data to XML?

[zeyu sun]

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

[Natalie Tasman]

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

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[Matt Chambers]

As Natalie suggested, Analysis.yep indicates the Bruker/Agilent YEP
format which ProteoWizard reads with CompassXtract. Msconvert will
automatically detect the format of the .d directory and use the
appropriate reader. Keep in mind the CompassXtract interface (which
supports Bruker FID/BAF and Bruker/Agilent YEP) is only licensed for
non-commercial use.

-Matt

>> *Command FAILED*

[Robert]

Hi,

I'm using CompassXport (Free download from Bruker, after
registration), not CompassXtract

>compassxport -multi d:\data\directory\

will convert all *.yep files of the given data directory to *.mzXML
files which can be read by TPP/X!Tandem. It will automatically dive
into your .D directories.

I used this tool successfully for converting data of the HCTultra/ETD
(Bruker) and the MSD/XCTultra (Agilent).

Those *.mzXML files work only for X!Tandem, not for OMSSA.

For generating *.mgf files usable for OMSSA searches I use
MzXML2Search, bundled with the TPP:

>FOR %I IN (*.mzXML) DO MzXML2Search -mgf -ACID -M2-2 -P5 -I0.01 -B10 -T5000.0 %I

converts all *.mzXML files to OMSSA compatible *.mgf

Saludos, Robert

On Feb 11, 1:04 pm, Matt Chambers <matthew.chamb...@vanderbilt.edu>
wrote: