Dear all,
I am trying to plot an LC-MS/MS dataset with the CID events and
peptide identifications (probabilities). It has worked for me in the
past, using Mascot and mzXML files made by Bruker's compassXport.
However, I do not seem to be able to get the peptide probabilities in
the Pep3D plot anym
Hi there -
Perhaps others have noticed this as well: when filtering a pepXML file
with regular expressions in the PepXMLViewer, the Viewer crashes (on
Windows systems - not on Mac according to Bjorn) with an error
"PepXMLViewer.cgi has encountered a problem and needs to close. We
are sorry for th
We have an opening in our group for a postdoc with a background in
computer science or bioinformatics and a track record in high-
performance computing and parallel algorithms. Experience with data
analysis in proteomics and tools such as those in the TPP, as well as
open formats for LC-MS(/MS) dat
Dear Folks,
Does anyone know if there is already a pepXML to/from mzIdent(ML)
converter out there (possibly requiring additional input)?
All the best,
Magnus Palmblad,
Leiden University Medical Center
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Dear all,
I know this is an old chestnut, but as I have easily been able to
solve it in the past, perhaps it is something new here as well. I have
configured $base_dir etc. in tpp_gui.pl to point to D: instead of C:
(other than this, the paths are identical). I also changed the TPP-
specific parts
Dear all,
We figured out the problem - the tpp_gui.pl has a regular expression
matching of directories that is case-sensitive, so D:\ is different
from d:\ from the TPP point-of-view (even if they are identical in
Windows). A small and very friendly suggestion would be to use uc( )
or something si
Dear all,
Problem solved - forgot TPP is case sensitive and D:\ not the same as
d:\. Changed all the settings and variables, and now it seems to work.
Cheers,
Magnus
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Dear All,
This may be primarily a question for Henry, but how is the specified
precursor m/z tolerance in the SpectraST Options used? We can see that
it has some effect, but it reports (good) PSMs with considerably
larger m/z errors. For instance, specifying a m/z tolerance of 0.1 Th
(too narrow g
Dear All,
We have a similar problem in that we don't see any retention times (they
are all zero) from the X!Tandem+Tandem2XML-generated pepXML files. This
problem appeared with the 4.6 version of the TPP with the updated X!Tandem,
previously we had no problems with it. For SpectraST we still ge
Dear All,
Does anyone know if there already is a converter for netCDF to mzXML or
mzML for LC-MS or LC-MS/MS data?
Cheers,
Magnus
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Hi Thomas,
Was the mzML file indexed or not? This can sometimes make a big difference
if the program you use accesses the data randomly (or one spectra at a
time). The mzXML files always have indices, but for mzML they are optional.
Then the mzML parser must also make use of the indices of cou
Absolutely right! I should have said that at least we encounter non-indexed
mzML files much more often than non-indexed mzXML files (for instance in
compassXport 3.0.5 the default is indices with mzXML, no indices with
mzML...). We did some benchmarking with our parsers and having the indices
d
Dear All,
This is a "favorite" problem among TPP users, and we thought we had solved
it once and for all. But with the new TPP version (4.6.0 and 4.6.1) there
are issues with some of the tools when working with data on another drive
(G: in our case). I have changed the WEBSERVER_ROOT environmen
Yes, and the mzXML decomposer is available here:
http://www.ms-utils.org/decomposition/. Please let us know if you encounter
some problems running it.
~Magnus
On Tuesday, 8 January 2013 17:57:40 UTC+1, Eric Deutsch wrote:
>
> There’s also a recent paper that describes such a strategy:
>
>
>
>
Dear All (especially David),
I am trying to use the ANN retention time predictor. The training runs OK,
but when trying to use it I get this error:
gsl: init_source.c:29: ERROR: vector length n must be positive integer
Default GSL error handler invoked.
This application has requested the Runtim
OK - I sent the training set and the ANN model by e-mail.
On Thursday, 28 March 2013 18:49:41 UTC+1, David Shteynberg wrote:
>
> Hi Magnus,
>
> Can you forward me the files you have and the commands you are using and I
> will debug?
>
> Thanks,
> -David
>
> On Thu, Mar 28, 2013 at 10:47 AM, magnu
Hi David,
Somehow I missed your reply (which was very quick). I will give it a try
now - thanks!
Magnus
On Thursday, 28 March 2013 22:28:34 UTC+1, David Shteynberg wrote:
>
> Thanks for the files you've provided. I was able to find and fix one
> error in the code. TPP revision 6171 from tru
Yep - this works fine, thanks!
Cheers,
Magnus
On Wednesday, 17 April 2013 17:49:46 UTC+2, magnus@gmail.com wrote:
>
> Hi David,
>
> Somehow I missed your reply (which was very quick). I will give it a try
> now - thanks!
>
>
> Magnus
>
> On Thursday, 28 March 2013 22:28:34 UTC+1, David Shte
Hi Eric,
We will be there with a large group this year (including four grad
students), and I'll make sure they all stop by your booth! :-)
Too bad the TPP workshop is scheduled the same evening as the
bioinformatics workshop arranged by Searle and Käll. That could have been
done better I think
Dear Sun,
I think QualScore is designed for exactly this purpose.
Cheers,
Magnus
On Monday, 8 July 2013 02:29:03 UTC+2, szyf...@gmail.com wrote:
>
> Dear TPP users,
> I'm wondering if there is any tools that can extract those spectra with
> high spectra quality but no hits from peptideprophe
Dear TPP developers and users,
I took the the new Comet in TPP 4.7 (POLAR VORTEX) out for spin, but keep
getting errors like "Error -
CometMemMgr::CometMemAlloc(pdTmpFastXcorrData[1374])" and "Operation not
permitted" when searching an mzXML made from some 5 GB Orbitrap E. coli
data. This mzXM
Hi Jimmy,
Many thanks - the "spectrum_batch_size" trick worked! Are the results (e.g.
the expectation values) dependent on the batch size?
Cheers,
Magnus
On Monday, 3 March 2014 19:05:21 UTC+1, Jimmy Eng wrote:
>
> Mangus,
>
> There's something broken with our latest Comet 2013.02 rev. 2 rele
Hi Kate,
The Apache timeout should not matter if you run in from the command line.
Are the file names very long? You may have an 8192-character limit on the
entire command...
Cheers,
Magnus
On Friday, 14 March 2014 16:52:40 UTC+1, Kate Mostovenko wrote:
>
> Hi all,
>
> Maybe somebody had a s
Hi David and Chih-Chiang,
The recent question was about modifications, which can in principle be
treated as different amino acids (which is exactly what they are). For
RTCalc and similar models, each modification needs to be present in 15-20
or so distinct peptides for the coefficients to start
Dear Robert,
Nice work - thanks for the ping! I like your new adjective, "TPPish". Our
Taverna workflows also tend to be very TPPish.
The modular design of the TPP with emphasis on standard data formats is a
perfect match (like Swedish meatballs with lingonberry jam) for the
scientific workfl
Hey guys,
Great work with the new TPP version! However, we are having issues with
PTMProphet in TPP 5.0.0 (TPP v5.0.0 Typhoon, Build 201610111222-7423
(Windows_NT-x86_64). Regardless of the data I try (iProphet files from
PeptideProphet files from Comet or X!Tandem phosphopeptide identification
To add a comment: the phenomenon happens for a few of the most abundant
proteins, having many peptides. The peptide abundances look OK in the
quantitation.tsv file, so I may be able to work around this by
recalculating the ratios from this file.
Magnus
On Wednesday, 8 August 2018 15:18:33 UTC+
Hi Kelly,
I noticed PeptideProphet reads in 4+, 5+ and 6+ but no 2+ or 3+ peptides.
This seems unusual. There are also more decoy hits than non-decoys, which
isn't what you (or PeptideProphet) want. Is this what you see in the Comet
results?
Cheers,
Magnus
On Monday, 11 March 2019 17:48:12
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