Hi Scott,
I just checked in a fix to this error in SVN. The problem was the spectrum
names were getting extra whitespace at the end in the .tandem files, which
were being propagated to the pepXML. The workaround that I committed trims
any extra whitespace surrounding the spectrum name. The fix
Are you looking for a tool to do this (and if so, command-line or GUI?)
or are you looking for an API?
-Matt
MichaE wrote:
> Dear group,
>
> I have a question. Is it possible to access the header information
> for each scan within a Thermo *.raw data set? Has anyone did that
> before for a la
Eric,
Many thanks for your reply. The first three points were more or less what I had
scribbled down as things to use to argue for a fully open source license. It's
very useful having them mentioned by yourselves as well. I've started the form
filling, so will keep my fingers crossed that we're a
Greg,
Thanks for your comments. I look forward to seeing the paper on the standards.
It's a mixed bag of instruments here, Orbitrap XL, ABI 4800, QTOF Premier,
Bruker HCT Plus, Bruker UltraFlex II, and an Agilent QTOF on the way. Since they
are distributed between two distinct facilities it's unl
Hi Dave, I would welcome additional thoughts, but here's what we have to
say:
1) You can argue that there is not significant commercial value in what
you've done. It's probably quite nice, but there are many existing open
source and commercial products with similar feature sets and trying to
make
I haven't done too much with iProphet yet, but I really need to get that
going asap. I've just been swamped with too much to do and then a vacation,
so now I should be able to get caught up. We are working on a paper or two
where we've done multiple search engines and multiple data analysis package
Greg,
Nice to know I'm not the only one. I've tried to structure our pipeline
in a generic fashion, and separate things out to conf files, but it's by
no means an example of pristine coding. Fingers crossed it would still
be of use to someone.
As an aside, I think I noticed on here that you'v
I've pretty much done the same thing also, but I wasn't planning on
releasing the code, as I've been lazy and hardcoded most of the information.
That and I have built my scripts around an Oracle database, which isn't
freely available, so it would take considerable coding to make it more
generic. I
Dear All,
Firstly, apologies that this is going to be a bit of a rambling post.
Over the past 12 months I've been working on what is effectively an
alternative interface to the TPP vs Petunia, tailored towards giving a
very simple front-end for users of our central proteomics facilities,
fully a
After installing the perl-devel rpm and a lot of perl modules I did
get TPP installed on ami-45e7002c (fedora 8 with java and tomcat).
I'm just running the binaries running without the web interface so I
think I'm all set now.
I do appreciate the offer Joe.
Thanks,
Bill
--~--~-~--~~
Dear group,
I have a question. Is it possible to access the header information
for each scan within a Thermo *.raw data set? Has anyone did that
before for a large-scale data set? I'd like to have this information
available for some reproducibility assessment.
Many Thanks,
Micha
--~--~---
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