: spctools-discuss@googlegroups.com [spctools-discuss@googlegroups.com]
On Behalf Of Jimmy Eng [jke...@gmail.com]
Sent: Thursday, May 02, 2013 9:16 AM
To: spctools-discuss@googlegroups.com
Subject: Re: [spctools-discuss] why I got this error information?
Eileen,
The + in the file names
Eileen,
The + in the file names is not a problem at this stage of processing
although it is a reserved character for a URL so you will have issues
visualizing results in the web interface. The - character is OK. For
future reference, it's not enough to simply change the pep.xml and mzML
file
Liam,
I have to ask this basic question ... can you confirm you have
/etc/apache2/sites-enabled/tpp-4.6.2? Either as a direct copy of
/etc/apache2/sites-available/tpp-4.6.2 or preferably as a symlink to
/etc/apache2/sites-available/tpp-4.6.2?
What does your apache error log indicate when you
Liam,
At this point, perl is not the issue for you; our problem is definitely
with your apache config. The WEBSERVER_ROOT environment variable should
point to your webserver's document root i.e. the directory that contains
the index.html file that says It Works!. Is it possibly /var/www/html?
log may have more information.
...fail!
What is going wrong? If I go to localhost in a web browser I still get It
works!.
On 21 April 2013 20:48, Jimmy Eng jke...@gmail.com wrote:
Liam,
At this point, perl is not the issue for you; our problem is definitely
with your apache config
, Liam Bell bell.l...@gmail.com wrote:
Where can I find what my WEBSERVER_ROOT variable has been set to? Which
configuration file is it in?
On 21 April 2013 21:25, Jimmy Eng jke...@gmail.com wrote:
Liam.
Your ServerRoot should probably still be /etc/apache2. ServerRoot is
the root
this be set?
Thanks for your help so far, I appreciate it.
On 21 April 2013 21:48, Jimmy Eng jke...@gmail.com wrote:
Liam,
Here's a snippet of what you posted 3 days ago. The entry SetEvn
WEBSERVER_ROOT. Set this to the same thing you have DocumentRoot set as
in apache2.conf.
On Thu, Apr 18
Is sudo make make install possibly equivalent to sudo make followed
by make install? If so, that explains the permissions issue with make
install. It's easy to test. Just do any of the following and see if the
copy permissions issue goes away
sudo make; sudo make install
or
sudo make
:_Installing_on_Ubuntu_10.04.3
for
setting up apache but now that does not seem to be working.
I'll take a look through the forums and see what I can find about the
matter...
Thanks everybody for your help so far!
On 18 April 2013 22:18, Jimmy Eng jke...@gmail.com wrote:
Is sudo make make install possibly
Damian,
I'll contact you offline to see if we can figure out what's happening.
Both Lorikeet and old Comet viewer access the underlying spectra in the
same way. So the fact that the old viewer is having an issue means that
Lorikeet will to.
- Jimmy
On Mon, Apr 8, 2013 at 12:15 PM, GATTACA
a beginner when it comes to code.
thank you again,
Philip
On Wednesday, 16 January 2013 19:55:58 UTC, Jimmy Eng wrote:
Philip,
I'm guessing you're specifying a small fragment_bin_tol value for the
high-res ms/ms spectra. This causes Comet (not all capitalized) to use a
ton of memory and you're
No, you can still view the results on a linux system by just clicking on
the .pep.xml and .prot.xml files. But to do this requires a change to your
apache configuration. Look at the README for instructions on mod_rewrite.
On Wed, Mar 27, 2013 at 5:47 AM, GATTACA dfer...@umich.edu wrote:
Yes
Brian,
Will not work; there's currently no way to specify multiple variable mods
on the N-terminus so you'll have to manage with some work-around. There
are plans to treat the terminal mods the same way as amino acid mods in the
code (and this was a good reminder to go implement it) but it will
to convert mzXML to dta files, please
find attached dta files for scan 3, they are quite different.
Thanks,
David
On Mon, Jan 21, 2013 at 1:08 PM, Jimmy Eng jke...@gmail.com wrote:
David,
ReAdW requires the corresponding XRawfile2.dll from Thermo's Xcalibur
software; it currently won't
ReAdW or msconvet to output raw file header information, such as method
used, serial number, processing mode, etc.
David
On Wednesday, January 16, 2013 9:43:47 AM UTC-8, Jimmy Eng wrote:
Yes, that is the standalone project which is now also used in the TPP.
For converting Thermo raw files
I just emailed you off-list regarding the x64 binary.
On Thu, Jan 17, 2013 at 4:56 AM, Philip Brownridge
philip.brownri...@gmail.com wrote:
Hello Jimmy, thank you very much for your quick reply! You're completely
correct about the fragment bin value, when I ran Comet (thank you for name
/
Cheers,
Eric
*From:* spctools...@googlegroups.**com [mailto:spctools...@**
googlegroups.com] *On Behalf Of *Jimmy Eng
*Sent:* Tuesday, January 15, 2013 9:18 PM
*To:* spctools...@googlegroups.**com
*Subject:* Re: [spctools-discuss] Re: JRAP question
At this point, you can
no longer supported? Could you point to the right person if
it still is.
Thanks,
David
On Wednesday, January 16, 2013 8:08:00 AM UTC-8, Jimmy Eng wrote:
I believe MzXML2Search currently uses the mzParser code which you can
find in MSToolkit.
On Tue, Jan 15, 2013 at 10:23 PM, David Zhao weizh
Philip,
I'm guessing you're specifying a small fragment_bin_tol value for the
high-res ms/ms spectra. This causes Comet (not all capitalized) to use a
ton of memory and you're just running out of memory.
On the following UWPR SEQUEST page, there's a table correlating a set of
fragment_bin_tol
wrote:
Thanks Jimmy! So it sounds like jrap is not being updated anymore. If i'd
like to keep up to date with a mzXML parser, which library should I follow?
Thanks,
David
On Tuesday, January 15, 2013 7:14:17 PM UTC-8, Jimmy Eng wrote:
I'm not a jrap user nor do I know what file are associated
Carlos,
Unless I don't understand how XPRESS currently runs, I don't believe it
will work on your separate light and heavy searches. This doesn't explain
the failure to run error but it's worth mentioning up front. XPRESS
expects a variable modification to denote the difference between your
Chris,
Try setting the msms_run_summary base_name and search_summary base_name
to the name of the mzXML file. In your example below, have both
base_name=e120823DC_EC_04and make sure e120823DC_EC_04.mzXML exists in
the same directory as the interact.pep.xml.
See if that works to allow you to
Zeyu,
Support for this new version of Comet is not in the released versions of
the TPP yet; looks like it's targeted for TPP 4.7. You'll have to build
PeptideProphetParser from trunk sources if you can't wait.
On Sun, Nov 18, 2012 at 12:29 AM, zeyu sun szy3...@gmail.com wrote:
Dear TPP team,
Maybe look into Mass++ that was first posted here on spctools-discuss
back in 2008::
https://groups.google.com/forum/?hl=enfromgroups#!forum/massplusplus
http://www.first-ms3d.jp/english/mass2
On Tue, Oct 23, 2012 at 4:15 PM, Gautam Saxena gsaxena...@gmail.com wrote:
Does anyone know of a tool
I'm not aware of any way to do what you want to do. And
realistically, support for this probably isn't going to occur anytime
soon just because it's not an analysis that's commonly done.
On Tue, Oct 2, 2012 at 2:42 AM, Maik Boehmer maik.boeh...@gmail.com wrote:
Hi,
for mass spec analysis of
FWIW, just doing something as simple as changing the name from
zz85-control-8-003-9 to zz85-control-8-003-9y allows the
conversion to go through fine. Hopefully someone with time will look
at the convoluted input handling in Tandem2XML as the logic being used
to parse input file name and
Jessie,
The spectral viewer tries to read the spectra in .mzXML, .mzML, .dta
or collection of .dta compressed into a .tgz archive. So it doesn't
assume your data is in a .tgz file, that was just one of the attempts
it went through to try and access the underlying spectral data to
display and
Ben,
Have you done anything special to handle the scan numbers (which
presumably are not consecutive anymore starting from scan 1) and the
scan index? If not, address those and re-test or find out if those
are important for MSGF-db.
On Thu, Jun 14, 2012 at 10:02 AM, Ben Temperton
Try re-generating the index at the end of the mzXML file after you
edit out the charge state. The TPP tools are failing to parse your
mzXML because the scan index is no longer valid. You can re-generate
the index using indexmzXML which is distributed with the TPP
as far as I know, the TPP quantification tools currently do not
support triplex SILAC analysis.
On Wed, Apr 4, 2012 at 2:58 AM, zeyu sun szy3...@gmail.com wrote:
Dear TPP team,
I wondering if I can get help from you to process one of my SILAC data set.
My experiment design is a SILAC-like
here's the parameter you want:
http://www.thegpm.org/tandem/api/pcsemi.html
On Wed, Mar 7, 2012 at 2:49 AM, Amit Yadav amit007thech...@gmail.com wrote:
Hi
Does anyone know how to conduct semi-tryptic searches in x!tandem(native or
k-score)?
I know about the refinement model but that limits
Rich,
Since no one else has responded, I'm staring at iTRAQ data I just
processed through Libra today and the intensities reported in the
pepXML file are exactly those that are in the corresponding mzXML. I
have never seen data where this is not the case which means something
went wrong
Shaun,
Multiple processing reading the same fasta file off of an NFS
partition has never really been a performance issue that I've ever
noticed through the years on different clusters (even pushing a
hundred processes accessing the same fasta). If this really is a
problem for you, the obvious
Cyrus,
For XPRESS, minimally you just need to specify:
- which residues are labeled
- the mass difference between the light and heavy forms of the label
We have the precursor m/z of the identified peptide and can calculate
the precursor m/z of the isotopic pair just by knowing which residues
are
From: spctools-discuss@googlegroups.com [spctools-discuss@googlegroups.com]
On Behalf Of Jimmy Eng [jke...@gmail.com]
Sent: Tuesday, October 18, 2011 1:41 PM
To: spctools-discuss@googlegroups.com
Subject: Re: [spctools-discuss] ASAP Ratiopeptideparse.exe
Thank Patrick Pedrioli; he was the one who fixed the bug!
On Fri, Oct 21, 2011 at 10:59 AM, Ping yanpp...@gmail.com wrote:
Thank you s much Jimmy. It works now!!
On Oct 20, 2:18 pm, Jimmy Eng jke...@gmail.com wrote:
There's been a fix checked in to the Sashimi subversion repository
so much and it works! I just tried one fraction and it works
perfectly!
So appreciate all of you for your kind help!
Eileen
From: spctools-discuss@googlegroups.com [spctools-discuss@googlegroups.com]
On Behalf Of Jimmy Eng [jke...@gmail.com]
Sent
There's been a fix checked in to the Sashimi subversion repository
that addresses a known issue with XPressPeptideParser. Hopefully that
fix addresses the issue you're seeing. If not, let me know.
Since you're using linux, build XPressPeptideParser from either the
trunk or branch4-5 code.
On
Eileen,
Thanks for documenting this problem; I just committed a fix to address
the issue. I'll send you a link to download a replacement windows
binary in a separate email offlist as soon as I get a chance to build
it on my windows box.
- Jimmy
On Tue, Oct 18, 2011 at 10:51 AM, Eileen Yue
Eileen,
Can you download the following executable and update your TPP binary
with this one:
http://proteomicsresource.washington.edu/dist/XPressPeptideUpdateParser.cgi
The files should go in c:\inetpub\tpp-bin\. Let me know if this fix
does not work for the problem you're experiencing.
-
I would hazard to guess that this spctools-discuss post is relevant
for you: http://bit.ly/ogXwK0
2011/10/13 Goran Mitulović gox...@gmail.com:
Hello,
I am trying to convert a Thermo .raw file to mzxml but the operation fails
with the following message:
# Commands for session CHRRESHT3 on
Oliver,
If you can make a dataset available (ideally a single raw file in xml
format and corresponding pep.xml), I can take a look.
- Jimmy
On Tue, Sep 6, 2011 at 5:11 AM, oschill...@gmail.com
oschill...@gmail.com wrote:
Dear all,
in some cases, XPRESS wrongly assigns heavy and light states
(-p). If I set it to 0
everything seems to be OK.
Are there any plans implement it in the XPressPeptideUpdateParser.cgi
as well?
Thanks,
Oded
On Aug 6, 4:30 am, Jimmy Eng jke...@gmail.com wrote:
Oded,
The Xpress values you see in the pep.xml file, which means those
viewed in the PepXML
message --
From: Jimmy Eng jke...@gmail.com
Date: Dec 21 2010, 8:16 am
Subject: XPRESS discrepancy between PepXML viewer and XPRESS viewer
To: spctools-discuss
Oliver,
I finally had a chance to revert to 4.3.1 on two machines (linux
windows desktop), runXPRESSon an old ICAT dataset
Looks like you are missing libgd-devel and libgd.
Install with some command like: yum install gd gd-devel
On Wed, Jul 27, 2011 at 7:14 AM, tiantian wenbos...@gmail.com wrote:
Hi all:
When I install linux(centos) , I got errors like below:
Quantitation/XPress/XPressPeptideUpdateParser/
Greg, the precursorCharge attribute is only present for data where the
charge state is present in the raw file. This usually is true for
FT/Orbi data but not normally with LTQ/Velos data.
Robert, the real question is what precursor charge would you want to
be associated with each ms/ms spectrum
I'm sure David will update PeptideProphet to recognize the different
search_engine attribute that your pep.xml files contain. But another
option for you if you want to use PeptideProphet right now is to
actually use the TPP's Sqt2XML program to translate your .sqt files to
.pep.xml. It's
I would set the Xpress mass tolerance to 1.0 for the LTQ data.
In Sequest, 'peptide mass tolerance' is the mass tolerance for the
calculated peptide mass, which is a function of MS1 precursor scan
accuracy, while 'fragment ion tolerance' is the mass tolerance applied
to the ms/ms fragment ions.
I checked in the updates digestdb sources yesterday to the Sashimi
SourceForge repository that will allow you to specify modified
residues. You can download a compiled windows binary here:
http://proteomicsresource.washington.edu/dist/digestdb.exe
The command line option to specify the mods is
Amit,
There's no functionality to specify fixed modifications in that
program at this point. But it's easy to do so I'll add the ability to
do so soon.
On Tue, Apr 26, 2011 at 6:16 AM, Amit Yadav amit007thech...@gmail.com wrote:
I am using digestdb.exe program that comes with TPP installation.
Also look into the difference between 'Alias' and 'ScriptAlias' in
your apache setting below; I think you want 'Alias' for the document
(data) directory remapping as ScriptAlias is meant for directories
that contain CGI scripts.
If you want to store your results in /tpp/data/, consider mapping
The problem is likely due to MSe spectra not being labeled as MS level
2 scans (ms/ms scans) in the mzXML file. Look for msLevel=
attribute in the file to see what MS level is assigned to these
spectra. If I had to guess, they are considered MS level 1 scans and
no distinction is made between
Christine,
As far as I know, such a converter does not exist at this point.
Hopefully someone can chime in if that's not the case.
- Jimmy
On Tue, Apr 5, 2011 at 7:33 PM, Christine Vogel vogel@gmail.com wrote:
Hi All,
Reposting Thomas' question from earlier -- what is a good converter
In case anyone out there is interested ...
St. Jude Children’s Research Hospital's proteomics core and the lab of
Junmin Peng currently has two bioinformatics positions available. If
you think you might be interested and want more information, check out
job #s 20477 and 20478 at
I'm stumped as I can't replicate the error. Ruby sent me her data and
I had no problems running Out2XML to generate the pep.xml file. Both
on a Windows box and under Linux.
- Jimmy
On Mar 1, 1:58 pm, Ruby rgund...@jhmi.edu wrote:
Hi-
I just downloaded the latest version of TPP this week, so
Ruby,
The problem likely has nothing to do with the -Etrypsin option in the
Out2XML command. Do you have a bunch of *.out files in the directory
c:\Inetpub\wwwroot\ISB\data\RG_81_2\
Are those files named something like RG_81_2.1.1.1.out?
- Jimmy
On Tue, Mar 1, 2011 at 1:58 PM,
XPRESS supports N15 metabolic labeling. I don't think ASAPRatio does
but it's possible that functionality was added recently w/o my
knowledge of it.
You're going to have to run 2 separate searches. One search will
measure the normal (or light) peptides; no modifications are
specified here. The
Andreas,
I didn't say it was going to be easy! :)
Here's an example Sequest pep.xml file:
http://proteomicsresource.washington.edu/dist/sequest.pep.xml
As Matt suggested, the search_score names will need to change
(xcorr_score to xcorr and delta_cn to deltacn). Additionally,
you'll probably
Andreas,
There's definitely no support for Crux in TPP 4.4.1 if that's what you
tried. The semi good news is that David does have code in the Sashimi
SourceForge repository to start supporting Crux so maybe it'll work in
the next full TPP release. You might be able to push analysis through
by
XPRESS had a bug in TPP 4.4.0 which was addressed in TPP 4.4.1. What
solution to what problem are you looking for?
On Tue, Jan 25, 2011 at 2:18 AM, furukie efur...@etc.a-star.edu.sg wrote:
Hi,
I managed to solve my problem and its running successfully! I am still
having slight problems with
There's no inherent limitation keeping the TPP's version of Tandem
from using 100% of your CPU. Did you set the spectrum, threads
parameter to 4 for your quad core CPU? Any chance you're disk or I/O
bound?
I can't help you with Tandem Cyclone TPP; it may work. Do a quick
search and see if
occurs when viewing a TPP 4.3
analysis with TPP 4.4. We have now rolled back to TPP 4.3 to keep our
XPRESS analysis consistent. Any advice on how to proceed in the
future?
Thanks
Oliver
On Nov 23, 5:46 pm, Jimmy Eng jke...@gmail.com wrote:
Oliver,
What parameters did you use to runXPRESS
It should be number(decoys)/number(targets) irrespective of
concatenated or separate searches.
On Wed, Nov 24, 2010 at 5:20 AM, Amit Yadav amit007thech...@gmail.com wrote:
Hi,
From what I understand, the simplest ways to calculate FDR using a
Target-Decoy search are:-
1. Run a Concatenate
Oliver,
What parameters did you use to run XPRESS? The GUI showing elution
profiles has no current support for the isotope option (summed
intensities of first N isotope peaks) but otherwise should return the
same ratios as that shown in the pepXML file.
- Jimmy
On Mon, Nov 22, 2010 at 5:09 AM,
also tried by using -L15000 in running mzXML2Search.exe but there
no difference in the scan count of mgf file.
with regards,
Jagan Kommineni
On Fri, Nov 5, 2010 at 1:56 PM, Jimmy Eng jke...@gmail.com wrote:
Jagan,
Start with your mzXML file. Generate mgf using MzXML2Search -mgf
As far as I'm aware, there's no tools that can do this. Hopefully others
can chime in if they know otherwise.
On Mon, Nov 8, 2010 at 7:59 PM, Jagan Kommineni
jagan.kommin...@gmail.comwrote:
I wonder whether these is any way possible to generate mzXML file from MGF
file to match the scan
I just tried readw on wine for the very first time this afternoon
(version 1.2.1 on a RHEL 5.5 box); I'm impressed with how easy it was
to setup. Both very old LCQ and new Orbi RAW files generated mzXML's
that were *exactly* the same between wine and native Windows
conversions. 'diff' returned
Similarly, if
only the difference between light and heavy residues are entered for
XPRESS, how does this program know the mass of the light and heavy
tagged residues?
Regarding this question, XPRESS doesn't need to know the mass of the
tagged residues as that information isn't necessary.
in
the pepXML file.
On Oct 22, 4:53 pm, Jimmy Eng jke...@gmail.com wrote:
Similarly, if
only the difference between light and heavy residues are entered for
XPRESS, how does this program know the mass of the light and heavy
tagged residues?
Regarding this question, XPRESS doesn't need
is heavy. Perhaps this is discrepancy that is causing me problems
with ASAP ratio. Should the MASCOT search be formatted such that the
light tag is a fixed modification and the difference between heavy and
light is a variable modification?
On Oct 22, 5:26 pm, Jimmy Eng jke...@gmail.com wrote
To keep everyone on the same page, even though this thread is
referring to building ReAdW in VC, I'm pretty sure David's successful
gcc/mingw builds refers to building the other TPP components and not
the mzXML converter that you're interested in.
On Tue, Oct 12, 2010 at 11:35 AM, Jeffrey Milloy
Lukas,
These tools could definitely be optimized and improved, especially for
high res data that didn't really exist when they were first developed.
That said, with respect to question 1, you're using two imperfect
tools on presumably large datasets so it's not surprising to see some
For any folks using XPRESS with the 4.4 release of TPP, I was recently
notified of a bug which I validated is present. A fix has been made
and is being tested. I would suggest not using this particular
version of the tool until the next maintenance release is out; revert
to the 4.3.1 binary if
Bjorn,
In the link to the plot-msms.cgi spectrum viewer, add Debug=1 to
the URL. This causes the CGI to not remove the intermediate files it
uses including the *.gp gnuplot script and the *.spec? files which are
the data files to plot (peak lists and peak annotations).
Do that once and then run
You did it all right. Can you check which version of gnuplot you have
installed? The TPP requires 4.2 and I suspect you might have an older
version installed.
Type 'gnuplot' on the command line to see what version you have.
'quit' will get you out of the gnuplot prompt.
On Wed, Aug 25, 2010
Ignore that message regarding the font (which you wouldn't normally see).
A set of Windows fonts are listed to be used if available for the text
in the plots; otherwise whatever default system font gets used for
non-Windows systems.
On Wed, Aug 25, 2010 at 12:56 PM, Bjorn caveman.bj...@gmail.com
Tom, possible there are no ms/ms scans in this raw file?
On Mon, Jul 19, 2010 at 2:01 PM, tommyg chunkeymonkeylo...@gmail.com wrote:
Hello,
I'm getting a No input spectra met the acceptance criteria error
while running the latest version of X!Tandem on a 64-bit Intel(R)
Core(TM)2 Duo CPU
fwiw, MzXML2Search does support mzML input files too.
On Wed, Jul 7, 2010 at 11:24 AM, Jesse J firstblackphan...@gmail.com wrote:
mzML is the new format that should be used, but I haven't seen any
programs out there that will convert mzML into mgf and ms2, like
MzXML2Search does with mzXML.
downloaded the MascotConverter.cxx source file.
How do I compile the MascotConverter file so that the TPP source file
dependencies are met?
On Jul 1, 12:35 pm, Jimmy Eng jke...@gmail.com wrote:
http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteom...
This just points
On Jun 30, 12:37 pm, Jimmy Eng jke...@gmail.com wrote:
You can use any prefix as long as it's consistent (and obviously
unique and not present in the target database entries). In the tools,
you will specify what prefix denotes the decoy entries. Like REV or
### or ###REV### ...
On Tue
I would be a little concerned with my files were transferred as xml
after mascot searching was done. What generated the xml files and in
what format are they? I believe that Mascot exported pep.xml files
won't run through the TPP correctly (but I could be wrong).
The only advice I can give you
There's no surprise that generating mgf files using other tools can
cause Mascot to perform (much) better as those tools apply things like
peak picking which MzXML2Search doesn't do. MzXML2Search pretty much
just takes the input spectral data and writes it back out into the
chosen output format.
here's one generated using default settings in the Libra condition
file generator that's available in the TPP GUI interface:
http://bit.ly/c7dsrO
On Thu, Jun 10, 2010 at 5:56 AM, hillan...@verizon.net
hillan...@verizon.net wrote:
List,
Can anyone point me to a Libra condition.xml file for
I just changed to a really big value. (9 was considered big many
years ago!)
On Thu, Jun 10, 2010 at 9:49 AM, Matthew Chambers
matthew.chamb...@vanderbilt.edu wrote:
Unless there are indeed downstream problems, it would be good to change that
default upper scan number since others are
It's not an error but rather a warning. The warning by itself doesn't
indicate a critical problem (although I suspect you might have other
problems). Take a look at your pep.xml file and see if it looks like
it has reasonable content in it.
Some things to note:
- your tandem input file should
oops - I just read your last note. Name your Tandem searches with an
extension.xtan.xml or just .xml; using .mzXML for those is asking for
trouble.
On Wed, May 5, 2010 at 2:43 PM, Jimmy Eng jke...@gmail.com wrote:
It's not an error but rather a warning. The warning by itself doesn't
indicate
The Tandem2XML program will try to read each scan's retention time
from the mzXML and add it to the resulting pep.xml. If not it can't
find the mzXML file, it issues the warning and leaves out the
retention time.
This warning does imply that the standard TPP convention of expected
files and
No, ReAdW does not have that functionality nor does any other software
that I'm aware of.
On Tue, Apr 20, 2010 at 11:44 AM, cfourn...@wesleyan.edu wrote:
Hi
Is it possible to use ReAdW from SPC to convert mzXML files back to the
original .RAW files. If not, does anyone know if this is
you can get trunk by subversion checkout:
svn co
https://sashimi.svn.sourceforge.net/svnroot/sashimi/trunk/trans_proteomic_pipeline
tpp-trunk
or just visit the URL below and select 'Download GNU tarball':
http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/
Sadly the need for manual inspection isn't going to go away soon but
things will get better with peak picking. I'll look into adding using
median instead of mean as a user option.
On Wed, Apr 7, 2010 at 12:44 AM, Oded oded.kleif...@gmail.com wrote:
Hi All,
Are there any planned improvements or
When a precursor charge is not known, the logic that is used to
analyze the data is as follows. If there are no peaks above the
precursor m/z then the spectrum is assumed to be 1+ and analyzed as
such. If there are peaks above the precursor m/z then the precursor
ion is assumed to be multiply
Andreas,
I don't believe Brian or any other helpful external person can access
the files when you place it in ISB's ftp site.
Anyways, the ramp parser is frail and finicky and expects an mzXML to
be formatted just the way it expects. Your modified mzXML has a lot
of formatting changes. The
byteOrder=network
pairOrder=m/z-intQ0BLmUBez4BDSRBhQQDRN0NN...w==/peaks
and then re-index.
On Tue, Mar 23, 2010 at 2:29 PM, Jimmy Eng jke...@gmail.com wrote:
Andreas,
I don't believe Brian or any other helpful external person can access
the files when you place it in ISB's ftp site.
Anyways
Here are the output columns. I just updated the source files in to
have the usage statement print these out for digestdb and make it
clearer for pep_dbcount.
digestdb output columns:
- peptide length
- protein reference
- peptide mass
- previous amino acid before peptide
- peptide sequence
-
I suggest you start debugging the problem one step at a time.
First confirm that your Tandem search actually ran by looking at
contents of the .tandem file.
Next, check contents of tandem.pep.xml.
Do both of these files look like they have peptide IDs in them?
On Wed, Mar 10, 2010 at 2:04 PM,
,
Amit Kumar Yadav
Senior Research Fellow (SRF-CSIR)
IGIB, New Delhi (India)
http://masswiz.igib.res.in
On Sat, Feb 27, 2010 at 4:22 AM, Omoruyi Osula oosu...@gmail.com wrote:
It worked. Thank you.
On 2/25/, Jimmy Eng jke...@gmail.com wrote:
You're calling it wrong (old style). Type
at 3:49 PM, Ping yanpp...@gmail.com wrote:
Thanks Jimmy!
Is there any sequest.params sample with modifications I can get?
Thanks again!
Ping
On Mar 3, 5:16 pm, Jimmy Eng jke...@gmail.com wrote:
unless there's a way to convert .msf to pep.xml, and I'm not aware of
any tool that does
...@web.de wrote:
My .out Data looks just like the .dta I posted.
But I found a sequest.txt file inside my .out DIR with the following
lines:
SEQUEST v.28, (c) 1998-2009
Failed to initialize FLEXnetWrapper
On 25 Feb., 17:29, Jimmy Eng jke...@gmail.com wrote:
There is no date/version information
unless there's a way to convert .msf to pep.xml, and I'm not aware of
any tool that does this, you'll have to go the .out route.
On Mar 3, 2:18 pm, Ping yanpp...@gmail.com wrote:
Hi All,
The output of the Proteome Discover is *.msf. Is there an easy way to
compute peptide prophet from it? Or
Look up accurate mass and time tags, peptide mass fingerprinting, and
maybe even a general proteomics data analysis review such as doi:
10.1038/nrm1468
I hope you don't take this too negatively but the scope of what one
might consider ms1 data is too general (a peptide mass fingerprint
spectra,
101 - 200 of 247 matches
Mail list logo
