We have released an update for the Trans-Proteomic Pipeline
(TPP) software, 4.2.x series, bringing the current version to 4.2
revision 1 (4.2.1). Releases are
available for native windows as well as linux and Mac OS X source from all the
usual locations (please see below).
Currently, the Agilen
Hello Andrej,
What version of the TPP are you working with, and on what system
(windows, linux, etc.)?
-Natalie
On Apr 8, 2009, at 1:41 AM, dre wrote:
>
> Hey guys,
>
> I have been working with TPP for some time now and recently I noticed
> the following bug. This is my workflow that results
Yes.
Let's continue technical discussions off this support list.
Best,
Natalie
On Apr 8, 2009, at 9:21 AM, Matthew Chambers wrote:
>
> Are those thresholds something you pass to the API?
>
> -Matt
>
>
> Natalie Tasman wrote:
>> Hi Ben,
>>
>> If you run trapper at the commandline without any a
Hello Ben,
Last year I spent quite a lot of time working with Agilent to exactly
replicate the behavior of their MassHunter mzData exporter, including
thresholding. I'm sorry that this isn't working for you. These
threshold flags should work. As you know from beta-testing the
converter,
Hi Federico,
If you're running with "Enchanced" mode, there is a fix in the
upcoming 4.2.1 version of the converter. Can you please check?
-Natalie
On Apr 8, 2009, at 9:20 AM, fto...@gmail.com wrote:
>
> Hi Natalie,
> today we did another step into the problems I mentioned above.
> It seems
Hi Natalie,
today we did another step into the problems I mentioned above.
It seems that my .mzXML file contained mslevels "0" and "1" instead of
"2" and when we substituted 0 with 2 it worked fine...we had the idea
from another prevoius discussion: ReadW getting msLevel="0" wrong
is there a perm
Are those thresholds something you pass to the API?
-Matt
Natalie Tasman wrote:
> Hi Ben,
>
> If you run trapper at the commandline without any arguments, it will
> give you all of the options, including thresholding both in absolute
> and relative terms.
>
> Please let us know how that works f
Hey guys,
I have been working with TPP for some time now and recently I noticed
the following bug. This is my workflow that results in the problem:
Thermo Orbitrap RAW file is inputted into tpp -> convert to mzxml ->
convert to mgf -> run mascot -> convert to pepXML
The problem is as follows:
Matt,
The data is from MassHunter so I have been using Trapper up to this point to
get mzXML files. Thanks for the tip regarding msconvert. I'll give this a
shot.
Natalie,
Thanks for the advice regarding the threshold usage. I have tried this out
but as far as I can tell its not doing anything. I'
