Announcing Trapper: Agilent MassHunter (.d)-to-mzXML converter

[Joshua Tasman]

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_id=284524

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 ("Petunia").


-Josh Tasman, July 17 2008 Seattle

[Spinnaker]

Josh,

I have encountered a bit of a probblem using this program with
windows vista. I when I input the following:

trapper --mzXML c:\msconvert\BSA000001.d c:\msconvert\BSA1.mzXML

I get the following error:

ERROR at .\MHDACWrapper.cpp, 60:
HR = -2147024894
OpenDataFile
unable to open c:\msconvert\BSA000001.d with MassHunter interface

what did I do wrong? you have any idea's?

Marcus

[Dani]

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

> http://sourceforge.net/project/showfiles.php?group_id=69281&package_i...

[Joshua Tasman]

Hi Marcus,

We don't have access to Windows Vista here for testing, but I can forward this to the Agilent team.  If possible, perhaps you could upload a small sample data file with this problem to our ftp server (see http://groups.google.com/group/spctools-discuss/web/how-to-upload-files-to-the-spc-team);

-Josh

[Joshua Tasman]

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

[Spinnaker]

Josh,

With respect to the fact that it's vista, I tried running trapper
on my spectrum Mill work station (Windows Server 2003) and like Dani I
got the same error. Anyway! here is the output from running the
program with verbose.

C:\Program Files\trapper>trapper --mzXML --verbose E:\msconvert\BSA1.D
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: E:\msconvert\BSA1.D
output filename: E:\msconvert\BSA1.mzXML

ERROR at .\MHDACWrapper.cpp, 60:
HR = -2147024894
OpenDataFile

unable to open E:\msconvert\BSA1.D with MassHunter interface

C:\Program Files\trapper>


The data I generate is from a Agilent 6330 (HPLC-ChipCube-ESI-Ion
trap) Is this data compatible with trapper? I will also try to upload
the file that I am working with.

Marcus


On Jul 22, 3:52 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
>

[Dani]

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:

> > > -Josh Tasman, July 17 2008 Seattle- Hide quoted text -
>
> - Show quoted text -

[Joshua Tasman]

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

[Josh T]

(This thread was continued on the spctools-discuss list. -Josh)


On Jul 22, 4:17 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
>

[KanshinED1]

Hi, guys.
It seems that I have exactly the same problem on Windows 2000 server
(data were generated on Agilent ESI ionTrap instrument):

C:\Program Files\trapper>trapper --mzXML -v E:\SpectrumMill\msdataSM
\Eugene\Sept
ember2008\17September2008\BSA_F1_F6.d E:\SpectrumMill\msdataSM\Eugene
\September2
008\17September2008\BSA_F1_F6.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: E:\SpectrumMill\msdataSM\Eugene
\September2008\17September2008\
BSA_F1_F6.d
output filename: E:\SpectrumMill\msdataSM\Eugene
\September2008\17September2008
\BSA_F1_F6.mzXML

ERROR at .\MHDACWrapper.cpp, 60:
HR = -2147024894
OpenDataFile

unable to open E:\SpectrumMill\msdataSM\Eugene
\September2008\17September2008\BSA
_F1_F6.d with MassHunter interface

> > > > - Show quoted text -- Hide quoted text -

[Natalie Tasman]

(I'm continuing this thread on spctools-discuss.

Natalie)