Thank you for this interesting discussion. My original point was to
say that data collected on the same type of instrument and searched
against the same database with the same parameters can be analyzed
together in PeptideProphet.
I accept your point that in the case of the additional models tha
I disagree that
"finding is that these datasets are not truly independent because as
you note if they
were truly independent datasets the probabilities would not change.
Different datasets that are collected on the same instrument (or same
type of instrument) already "interact" with each other in
I don't agree that any hidden links are introduced, rather some
incorrect assumptions are exposed. When datasets are analyzed
together this is very explicit. When you are expecting that these
datasets should be independent but you are finding that you get
different results when you are analyzing
For two independent experimental data probability of particular scan
to match particular peptide should not depend on data in second
independent experiment that is why they are independent experiments.
With PeptideProphet when you combine two data sets in interact.xml and
process them together you
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PeptideProphet compute a probability that a PSM is correct GIVEN the
data. So I am not sure I understand what you mean exactly when you
say that this is "mathematically wrong". It is not correct to compare
probabilities on the same spectrum between different runs of
PeptideProphet when you give
Good advise David:
But,combining data from several independent analysis of similar
samples does not save the day. In fact one "bad" (from point of view
of PeptideProphet) msms-run can spoil the rest of data. And, in fact
it does. It does not sound right to me when estimation of peptides
probabil
Hello Anand and Sergey,
Negative values are placeholders to identify potentially correct PSMs
when there is too little data, insufficient separation between
positive and negative distributions in the model, or non-bimodal
search results (often a result of bad search parameters missing static
mod.
Hi Sergey,
Thanks for the explanation of your correspondence. It is definitely
true that the TPP could use additional documention. However, as you
know, we are a small group of developers and we try to support the
community as best as we can. Pragmatically we encourage our users to
refer to th
Dear Natalie:
>From personal communication of Anand to me : "But after MSMS file for
single protein fragment peak I could neither get the models but an
error saying no data quitting that happens at the protein prophet
level.After the peptide prophet probabilities are observed on few
occasions to
I have solved it. The prgram mzXML2Search have been installed follow
by TPP installed.
Thank your very much for your kind.
Bright
On 2月17日, 上午2时13分, Matthew Chambers
wrote:
> It depends what you want to use the MGF for. I think the TPP pipeline
> for the near future should continue using mxXML2
Hello,
This program is part of the standard TPP installation. It should be
in C:\Inetput\tpp-bin, after a successful installation.
Natalie
On Mon, Feb 16, 2009 at 8:01 AM, Bright wrote:
>
> Could someone direct me to where to download where to download
> mzXML2Search?
> I can't seem to find
Strange. What does perl -v report? It sounds like it may be a
corrupted install. Perhaps you could try rebooting, temporarily and
safely disable any active antivirus/security software, and try
reinstalling?
Best,
Natalie
On Mon, Feb 16, 2009 at 1:38 PM, tom.b...@gmail.com wrote:
>
> I insta
Hi Kris,
No one has been able to solve your specific program because no one has
tried the exact setup that you have, which is trying to run Thermo's
Proteomics Browser Suite, requiring the TPP to use the unsupported IIS
webserver. As you've found, the TPP can work with IIS, but we're not
able to
Hello Arand,
You'll need to start by converting the Shimadzu-specific instrument
files to mzXML or mzML files in order to use the TPP tools. The
SPC/TPP tools do not support this directly, but someone posted to our
list mentioning the Mass++ program which is advertised to do this:
http://groups
I have solved it. The prgram mzXML2Search have been installed follow
by TPP installed.
Thank your very much for your kind.
Bright
On 2月17日, 下午10时04分, Matt Chambers
wrote:
> Do you mean mzXML2Search instead of Mascot2XML? I agree that spectrum
> averaging should be a more universal feature; it's
I have solved it. The prgram mzXML2Search have been installed follow
by TPP installed.
Thank your very much for your kind.
Bright
On 2月17日, 下午7时33分, Bill Nelson wrote:
> We were never able to switch one of our labs over to TPP because they
> use ABI Q-TOF with Mascot and the Mascot daemon prod
Dear mzWiff developers,
I would like to ask if there will be a feature someday in mzWiff to
merge the single precursor scan files, which are output as *.mzXML
when inputting a multiple precursor ion scan *.wiff file, into one
*.mzXML file. Or maybe, I just didn't find the right option?
regards,
I have solved it. The prgram mzXML2Search have been installed follow
by TPP installed.
Thank your very much for your kind.
Bright
On 2月17日, 上午1时52分, "Brian Pratt" wrote:
> The msconvert tool should handle that:
>
> To convert foo.mzxml to foo.mgf
>
> msconvert --mgf foo.mzxml
>
>
>
> -Origi
Dear Anand
PeptideProphet is unable to estimate peptide probabilities in your
case and it will never will be able to do so no matter what you do. It
is a limitation/bug of PeptideProphet algorithm as far as I can tell.
But I wonder what kind of response, if any, you will get from folks
from Instit
Could someone direct me to where to download where to download
mzXML2Search?
I can't seem to find one .
Thanks
-Bright
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Do you mean mzXML2Search instead of Mascot2XML? I agree that spectrum
averaging should be a more universal feature; it's something I plan to
put in msconvert but haven't gotten around to yet. What range of
settings did you try for spectrum averaging in mzWiff?
-Matt
Bill Nelson wrote:
> We w
Hi all ,
I have been trying to upload and analyze a single protein MSMS CID
data retrieved from shimadzu instrument and I am unable to run the
pipeline.The pipeline fails at the protein prophet level and cites
error message "No data quitting". I tried also converting mzXML files
to dta as well as
We were never able to switch one of our labs over to TPP because they
use ABI Q-TOF with Mascot and the Mascot daemon produced an MGF file
that searched much better that the MGF file produced by mzWiff &
Mascot2XML. Through postings on this forum we learned that the better
performance (about 20%
I install active state perl. That seems to go well, perl is in my path
and perl -v gives a message
Then I run TPP_setup_v4_1_jetstream_rev_1
goes well till it looks for perl then shows an error
running c:/Inetpub/tpp-bin/which.exe also gives an error, no message
just the MS crash reporter
Any
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