massWolf

[fabien]

Hi, this is my first mail to the spc discuss list.
I am looking for a way to read Waters MassLynx Raw files for LC/MS/MS
data. I have been looking at massWolf which seems to do this kind of
job, provided the user have the DAC library installed. I would like to
know what is the status of massWolf development, e.g. still actively
maintained? future work? etc...
Are Waters people keen to help you by providing information about how
to use the DAC library, or you just hack the dll?


All the best,
Fabien

[Matthew Chambers]

I think it's safe to say that massWolf is out of beta, but development
is continuing as necessary. The crucial thing is that MassLynx doesn't
provide the peak processing that ProteinLynx Global Server does. Waters
is working on an mzML exporter out of PLGS, but there is no easy
programmatic access to PLGS like the DAC. :(

-Matt

[Fabien Fontaine]

Ok,
I am gonna try to use it then. I have downloaded a copy of the main
trunk on my XP win_32. I now want to compile the tpp tree. I can't
manage to build the boost library. I have unzipped the directory
boost_1_35_0 in win_lib
Then I've tried to run build_boost_v8.bat in directory win_lib but
bjam return the following error:
unable to find file or target named /zlib123-dll/adler32.c
It's look like a path problem, I could provide '.' as first argument
to the build_boost_v8.bat file but it seems that bjam request linux
style path.
Any hint?

Thanks,
Fabien

2009/3/2 Matthew Chambers <matthew....@vanderbilt.edu>:

[Natalie Tasman]

Hello Fabien,

massWolf has been a stable component of the TPP for quite a while for
DDA MS/MS file conversions. Of course, there are changes to be made
as the vendor software changes, and we do our best to stay up to date.
There are some important missing components, such as precursor charge
state extraction, due to limitations of the Waters software API (the
DAC), but we still routinely use this for our daily production work.

There is no need for you to download and build the sourcecode
yourself. You can download standalone binaries, or the entire Windows
TPP which includes a web-based GUI for batching conversion jobs (in
addition to much more).

Please see the latest TPP announcement email for download instructions
(http://groups.google.com/group/spctools-discuss/browse_thread/thread/a75b99f29c49ee98/845ace41d79afb83?lnk=gst&q=4.2.0#845ace41d79afb83)
for either option, and let us know how it goes.

Best,

Natalie

[Fabien Fontaine]

Thanks Natalie,
I'll leave compilation for later.
I have downloaded massWolf from the Sashimi page. For now It should be
enough. I have still to test it with a Raw file.

My best,
fabien


2009/3/2 Natalie Tasman <nta...@systemsbiology.org>: