spctools-announce Google Group

Feature addition to PIPE - Add GO Annotations

2008-09-02T21:55:41Z

Hi All,

I added a new feature to the PIPE as per a user's suggestion last
week. You'll find it in the "Operations" menu item. It is labeled
"Add GO Annotations". Using it, you are now able to retreive GO terms
based on their category (biological process, cellular component, etc)
AND by level (go levels 1 - 14). Also, and I suspect this will be the

Re: name change

2008-08-26T11:36:46Z

Dear Natalie

I just downloaded and installed trapper

When trying to convert a file I get the following (using the verbose
function)

I guess the problem is "unknown instrument type:5". The data comes
from an Agilent 6410 triple quad (the particular file being a selected-
ion modifying run).

SPC Tools Posters at World HUPO next week

2008-08-13T23:42:21Z

This upcoming week, the SPC software tools team will be presenting
two posters at HUPO's 7th World Congress in Amsterdam: one on
iProphet, presented by David (P-TUE-181), and the other on new TPP
functionality, presented by me, Luis (P-TUE-163).
Please feel free to drop by and say hello to me and David, and bring

name change

2008-08-13T23:29:35Z

Hi all,
Just letting you know that I have changed my name from Josh to
Natalie. I look forward to continuing to work with all of the great
people here in our proteomics software community.
Best,
Natalie

Re: [spctools-announce] Trapper on Win64bit Problem

2008-08-01T17:46:36Z

Hi Manfred--
I'll reply to the spctools-dicuss group so that this reaches a larger audience.
Josh

Trapper on Win64bit Problem

2008-08-01T03:01:01Z

Hi,
I installed the Trapper on a WinXP 64bit computer, looks ok. But when
I start to convert a file from AGILENT's QTOF, with the ChipHPLC, I
get the following error:

This application has requested the Runtime to terminate it in an
unusual way. Please contact the application's support team for more

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

2008-07-24T22:00:31Z

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

On Jul 22, 4:17 pm, "Joshua Tasman" <jtas...@systemsbiology.org>
wrote:

Re: interesting subversion news

2008-07-24T21:59:40Z

(sorry for any confusion; this was meant to go to our developer list :)
-Josh)
On Thu, Jul 24, 2008 at 2:09 PM, Joshua Tasman <jtas...@systemsbiology.org>
wrote:

Re: interesting subversion news

2008-07-24T21:09:07Z

Other interesting features (integrated with tortisesvn 1.5, too): selective
checkout, if you don't need the whole repository and changelists.
On Thu, Jul 24, 2008 at 2:07 PM, Joshua Tasman <jtas...@systemsbiology.org>
wrote:

interesting subversion news

2008-07-24T21:07:21Z

I just learned about an improved merge system appearing in subversion 1.5
that might make our lives a lot easier. Looks like there are still bugs to
be ironed out, but definitely something we should keep an eye on. SF has
some functionality to update the repository to 1.5, but I don't want to do
that yet (especially as they're still unstable in general)

Re: [spctools-announce] Re: Announcing Trapper: Agilent MassHunter (.d)-to-mzXML converter

2008-07-22T23:17:30Z

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

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

2008-07-22T22:07:26Z

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

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

2008-07-22T21:09:40Z

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

Re: [spctools-announce] Re: Announcing Trapper: Agilent MassHunter (.d)-to-mzXML converter

2008-07-22T19:52:45Z

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

Re: [spctools-announce] Re: Announcing Trapper: Agilent MassHunter (.d)-to-mzXML converter

2008-07-22T19:51:37Z

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
[link]