Dear Eric
I see now the same thing:
$ /home/hr/openmsall/source/THIRDPARTY/Linux/64bit//spectrast -V
-sLtestLib.splib spectra.mzXML
SpectraST started at Sat Oct 21 02:18:54 2017.
VERBOSE MODE...
Library File loaded: "testLib.splib".
Sorting query spectra in all mzXML files by precursor m/z before
Hi
One way to combine search engines outside the MaxQuant environment with
good quantification algorithms is the OpenMS package. This might be a
sensible way to go if you like to combine multiple search eninges and the
TPP search workflow with an alternative open-source quantification engine.
I am
Hi Zhang
This looks like a proteowizard error during conversion in the
SpectrumList_Thermo, so I am cross-posting this to the proteowizard support
list (supp...@proteowizard.org).
Hannes
-- Forwarded message --
From:
Date: 12 June 2014 03:53
Subject: [spctools-discuss] Thermo
Hi Krishan
there is quite an extensive documentation on the wiki, did you already
check whether your problem is answered there? See
http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST
I am not a developer of SpectraST but a fellow user. Maybe if you post
your problem, somebody
Hi Rachel
sorry, I dont know enough about the TPP and these programs to answer
these questions. However, there are multiple translation tables but I
guess that most of the tools would use the canonical one.
Maybe you should try the spctools list?
Hannes
On 29 April 2014 05:38, Rachel wrote:
>
Dear Bo
One software useful for this purpose is Mayu, see
http://proteomics.ethz.ch/muellelu/web/LukasReiter/Mayu/ or the TPP
(it should be packaged with the TPP).
Hannes
On 24 April 2014 15:53, Bo wrote:
> Hi,
> Does anyone know TPP how to calculate the PSM-level FDR and peptide-level
> FDR?
>
Hi Rachel
Abacus and Qspec are for spectral count label-free quantification, if
you want MS1 intensity-based quantification you might want to look
into SuperHirn
http://tools.proteomecenter.org/wiki/index.php?title=Software:SuperHirn
or OpenMS http://openms.de packages.
Hannes
On 22 April 2014
Eric
>
>
> -Original Message-
> From: spctools-discuss@googlegroups.com
> [mailto:spctools-discuss@googlegroups.com] On Behalf Of Hannes Röst
> Sent: Friday, April 04, 2014 1:27 AM
> To: spctools-discuss@googlegroups.com
> Subject: Re: [spctools-discuss] Can PeptideProphet and
oy to non-decoy ratio is satisfactory for FDR modelling, in
> your experience?
>
> Vadim
>
> On Apr 3, 2014, at 11:28 AM, Hannes Röst wrote:
>
>> Hi Vadim
>>
>> This will most likely _not_ work. It would probably be better if you
>> do not filter before xin
Hi Vadim
This will most likely _not_ work. It would probably be better if you
do not filter before xinteract but give it the full X!Tandem output
and then filter afterwards based on the computed probabilities. This
way you also might increase the total number of retained hits at a
fixed FDR.
Hann
Hi Luciana
One tool that might fulfil criteria 1 would be Mayu that is also part
of the TPP, see
http://proteomics.ethz.ch/muellelu/web/LukasReiter/Mayu/ - it will
calculate a new PSM score cutoff based on the input data (using the
decoys) and compute a PSM score cutoff that is equivalent to a cer
The main error seems to be that the processing engine is not recognized
running: "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.pep.xml'"
(OpenMS/ConsensusID)
error: engine OpenMS/ConsensusID not recognized
which seems to result from the attribute
search_engine="OpenMS/ConsensusID"
how
Hi Jason
We just completed the final release last August and published the
paper these days, so pyOpenMS has not been around that long. I hope it
is useful and stays useful to the community. If you have comments or
suggestions, please just send me an email :-)
Hannes
On 22 January 2014 19:41, J
Hi Liang
For easy handling of mzXML, you can also use pyopenms
import pyopenms
exp = pyopenms.MSExperiment()
pyopenms.FileHandler().loadExperiment(filepath, exp)
for spectrum in exp:
for peak in spectrum:
print peak.getMZ(), peak.getIntensity()
It is based on the OpenMS package and is avai
Hi
There is a .xsd file that specifies and documents the meaning of the tags
http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_3.2.xsd
in this case the sha1 of the current mzxml file is defined as
"sha-1 sum for this file (from the beginning of the file up to (and
including) the op
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