trapper error: can't open .d folder

[Joshua Tasman]

Hi Dani,

Yes, please upload a zipped file containing the entire .d folder and I'll see how it looks on my system.  Hopefully we can get you working soon.  Also, please let me know the exact version number of your MassHunter acquisition software.

-Josh

On Thu, Jul 24, 2008 at 3:36 PM, Dani <danie...@hotmail.com> wrote:

HI Josh,

I have a new agilent QTOF, I am working under MassHunter platform and
the .d files are the new .d files. So, it must be some other bug. If
you want I can give you some of my data or you can give a dataset, and
maybe you will be able to see the reason.

Thanks a lot

Dani

On Jul 24, 2:58 pm, "Joshua Tasman" <jtas...@systemsbiology.org>
wrote:

> Hello Marcus (and Dani),
>
> I see the problem: You're using Agilent Chemstation .d files, which are not
> compatible with the MassHunter .d format.  Agilent can best answer questions
> about the Chemstation format; I've never seen it or worked with Chemstation
> before, myself.
>
> Dani, inside the .d folder, if you see ".yep" files, you're also dealing
> with the Chemstation format.
>
> Sorry for the trouble, and please post to the list if you find a usable
> solution.  The Bruker program "CompassXport" (you can find some info on this
> on our wiki) may be able to deal with the .yep format, but I'm not sure if
> it takes the .d Agilent folder format.
>
> Josh
>
>
>

> On Thu, Jul 24, 2008 at 8:58 AM, Spinnaker <mmmano...@gmail.com> wrote:
>
> > Josh,
>

> >  OK so I uploaded the files to website, here is the URL:
>

> >http://www.mediafire.com/?sharekey=91282cb11d4582a0d5a101cf914073b47c...

>
> >  Hopefully this works.
>
> > Marcus
>
> > On Jul 23, 5:25 pm, "Joshua Tasman" <jtas...@systemsbiology.org>
> > wrote:
> > > Hello Marcus,
>
> > > Unfortunately I didn't find your upload.  Alternatively, you could try
> > > uploading to the "files" section of this newsgroup's website (and we can
> > > delete afterwards), or post it somewhere yourself and send me a URL.
>
> > > Josh
>
> > > On Tue, Jul 22, 2008 at 6:09 PM, Spinnaker <mmmano...@gmail.com> wrote:
>
> > > > Josh,
>
> > > >    I don't know what you mean by small file, however I am uploading a
> > > > file/folder called BSA1.D it's just BSA as a calibration.
>
> > > > Marcus
>
> > > > On Jul 22, 7:17 pm, "Joshua Tasman" <jtas...@systemsbiology.org>
> > > > wrote:
> > > > > Thanks to both Dani and Marcus for the feedback.  Honestly I'm not
> > sure
> > > > what
> > > > > the issue is; I assume that the Agilent MHDAC library is compatible
> > with
> > > > all
> > > > > MassHunter-compatible instruments, but I don't know specific
> > instrument
> > > > > models.
>
> > > > > Probably the best way to proceed is to upload small test files and
> > I'll
> > > > try
> > > > > to reproduce here.
>
> > > > > Thanks for the feedback, and hopefully we can get this working soon.
>
> > > > > Josh
>
> > > > > On Tue, Jul 22, 2008 at 3:07 PM, Dani <danielit...@hotmail.com>
> > wrote:
>
> > > > > > Hi Josh,
>
> > > > > > Here is the output, and of course I can run small test raw file.
>
> > > > > > c:\Program Files\trapper>trapper  --mzXML -v C:\Program
> > Files\trapper
> > > > > > \080721_apo
> > > > > > myoglobin_pepsin2ul_Frag0004.d C:\Program Files\trapper
> > > > > > \080721_apomyoglobin_peps
> > > > > > in2ul_Frag0004.mzXML
> > > > > > 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:\Program
> > > > > >  output filename: Files\trapper
> > > > > > \080721_apomyoglobin_pepsin2ul_Frag0004.d
>
> > > > > > ERROR at .\MHDACWrapper.cpp, 60:
> > > > > > HR = -2147024894
> > > > > > OpenDataFile
> > > > > > unable to open C:\Program with MassHunter interface
>
> > > > > > Cheers
>
> > > > > > Dani
>
> > > > > > On Jul 22, 12:52 pm, "Joshua Tasman" <jtas...@systemsbiology.org>
> > > > > > wrote:
> > > > > > > Hello Dani,
>
> > > > > > > Thank you for the positive comments, and I'm sorry to hear that
> > > > you've
> > > > > > > having trouble.  Can you please copy the entire output from
> > running
> > > > the
> > > > > > > program with "-v" (verbose), and consider uploading a small
> > sample
> > > > > > problem
> > > > > > > file (please see the reply to Marcus)?
>
> > > > > > > Josh
>
> > > > > > > On Tue, Jul 22, 2008 at 12:16 PM, Dani <danielit...@hotmail.com>
> > > > wrote:
>
> > > > > > > > Hi Josh,
>
> > > > > > > > These is a crucial application for me, I am happy to see that
> > > > someone
> > > > > > > > has written this comverte. By the way, I am having the same
> > problem
> > > > as
> > > > > > > > Marcus, although I am running in a Windows XP.
>
> > > > > > > > Thanks
>
> > > > > > > > Dani
>
> > > > > > > > On Jul 17, 3:58 pm, "Joshua Tasman" <
> > jtas...@systemsbiology.org>
> > > > > > > > wrote:
> > > > > > > > > I am very pleased to announce the public release of the mzXML
> > > > > > > > > converter for Agilent MassHunter raw data (.d directories),
> > > > called
> > > > > > > > > "trapper" (as a play on the word "hunter").  This release is
> > the
> > > > > > > > > result of a more than year-long collaboration between Agilent
> > and
> > > > the
> > > > > > > > > Aebersold Lab Seattle (SPC/ISB), which included extensive
> > on-site
> > > > > > > > > testing at a collaborating lab, and involved several
> > enhancements
> > > > to
> > > > > > the
> > > > > > > > > Agilent MassHunter Data Access Component ("MHDAC") used for
> > this
> > > > > > > > > converter.  Agilent has been extremely helpful, supportive,
> > and
> > > > > > > > > responsive throughout this work.  In fact, *Agilent is now
> > the
> > > > first
> > > > > > > > > and only instrument vendor to allow us to distribute the
> > required
> > > > > > > > > vendor API files along with a SPC converter*.  This means
> > that
> > > > anyone
> > > > > > > > > can now use Agilent's MassHunter files with the TPP, without
> > any
> > > > > > > > > requirement that the full MassHunter application be installed
> > on
> > > > the
> > > > > > > > > same machine.  Agilent recognizes that their customers may
> > have
> > > > > > > > > existing workflows, using tools such as the TPP, and support
> > for
> > > > open
> > > > > > > > > data formats like mzXML and mzML is increasingly essential
> > for
> > > > > > > > > archiving, sharing, processing, and publishing data.
>
> > > > > > > > > A new experience, for both our lab and the people at Agilent,
> > was
> > > > the
> > > > > > > > > combination of open-source and proprietary code.  The TPP,
> > > > including
> > > > > > > > > the core trapper code, is written under the LGPL license.  In
> > > > order
> > > > > > to
> > > > > > > > > prevent any possible implication that the LGPL would require
> > > > Agilent
> > > > > > > > > to expose the source code for any of their files, we worked
> > > > together
> > > > > > > > > to come up with a new architecture for the trapper converter
> > that
> > > > > > > > > completely insulates Agilent (only Apache-licensed wrapper
> > code
> > > > > > > > > directly accesses Agilent's API).  Neither the Aebersold Lab,
> > the
> > > > > > ISB,
> > > > > > > > > or myself (the author) has any desire to require Agilent to
> > > > release
> > > > > > > > > the source code for any of the related Agilent code for this
> > > > project.
>
> > > > > > > > > Please note, you may not redistribute the Agilent MHDAC
> > files.
> > > > > >  Please
> > > > > > > > > contact Agilent directly with any questions about
> > redistributing
> > > > or
> > > > > > > > > accessing this API for any other project or purpose.
>
> > > > > > > > > A note on version number: While this is initial release, the
> > > > version
> > > > > > > > > is 4.1.0-pr.  As the converters are integral components of
> > the
> > > > TPP,
> > > > > > > > > their version matches the main TPP version number.  Trapper
> > will
> > > > be
> > > > > > > > > released as part of the next major TPP release, 4.1.0 (I've
> > > > chosen to
> > > > > > > > > release the stand-alone version now in order to make it
> > available
> > > > as
> > > > > > > > > soon as possible.)  "pr" designates that this is a
> > "pre-release"
> > > > > > > > > before the main 4.1.0 release; it is not meant to construe
> > any
> > > > beta
> > > > > > > > > status for the trapper converter itself.
>
> > > > > > > > > Special thanks to the people at Agilent who made this happen:
>
> > > > > > > > > Malini Srikantarajeurs
> > > > > > > > > Heloise Logan
> > > > > > > > > June Bouscaren
> > > > > > > > > Frank Kuhlmann
> > > > > > > > > Joe Roark
> > > > > > > > > and everyone else on the Agilent MassHunter/QTOF teams who
> > > > supported
> > > > > > > > > this project
>
> > > > > > > > > And to our collegues in Zurich at the IMSB at ETH:
>
> > > > > > > > > Clementine Klemm
> > > > > > > > > Lukas Mueller
> > > > > > > > > Reto Ossola
> > > > > > > > > Damaris Bausch
> > > > > > > > > Bernd Wollscheid
> > > > > > > > > Bruno Domon
> > > > > > > > > everyone else who helped test and give feedback on the
> > converter.
> > > > > > > > > And of course Ruedi Abersold for his support of this project.
>
> > > > > > > > > Project development was supported by the Seattle Proteome
> > Center,
> > > > > > > > > funded under NHLBHI contract NO1-HV-28179.
>
> > > > > > > > > ==Installation instructions==
>
> > > > > > > > > Download and run the trapper_setup.exe installation file,
> > which
> > > > > > > > > contains the trapper executable ("trapper.exe") as well as
> > the
> > > > > > Agilent
> > > > > > > > > MHDAC files, from:
>
> >http://sourceforge.net/project/showfiles.php?group_id=69281&package_i.
> > > > ..
>
> > > > > > > > > The MHDAC files will be automatically installed and
> > configured.
> > > > > >  Files
> > > > > > > > > will be installed to the "trapper" directory under "Program
> > > > Files"
> > > > > > > > > (usually "C:\Program Files").  Neither mzXML internal data
> > > > > > compression
> > > > > > > > > ("-z") nor the mzML 1.0 standard ("--mzML") is supported in
> > this
> > > > > > > > > release, but will be in an upcoming release.  Full mzML 1.0
> > > > support
> > > > > > is
> > > > > > > > > planned by the end of July.
>
> > > > > > > > > A uninstaller is provided, from the "trapper" group in the
> > start
> > > > > > menu.
> > > > > > > >  You
> > > > > > > > > should use this program to cleanly unregister and remove the
> > > > Agilent
> > > > > > > > > MHDAC files as well.
>
> > > > > > > > > The converter itself is run from the command line, just like
> > all
> > > > of
> > > > > > > > > the other SPC converters.  Invoking the program without
> > arguments
> > > > > > > > > gives a usage statement.  The upcoming 4.1.0 TPP release will
> > > > also
> > > > > > > > > allow running the trapper from the TPP web interface
>

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