New TPP Release: Version 3.2.0 SQUALL
Joshua Tasman
We are releasing the next revision of the Trans-Proteomic Pipeline,
version 3.2.0 - SQUALL (cygwin package ISB-MS-Tools-3.2-0a; please note,
the cygwin distribution name now follows the current TPP version). This
update includes the following changes and improvements:
Cygwin Developer Tools:
o Based on feeback, the dev tools are now an *optional* part of the
installation. To include these, go to the "proteomics" section in the
installer and choose the "ISB-MS-Tools-dev" package.
PeptideProphet:
o Beta Phenyx support
- support of .pepXML Phenyx output extension
- users must specify xinteract options via commandline:
-D<database path>
-a<datapath>
o XTandem tuning of Discriminant Function Mixture Modeling
o More intuitive reimplementation of Gamma Distribution
o Auto skipping over files that have PeptideProphet results or aren't
pepXML
Performance optimizations for Q3ProteinRatioParser and
XpressProteinRatioParser from LabKey:
o 257x speed up on a 1.8MB Xpress protXML file, 1025x speedup on a 13MB
Q3 protXML file, 3495x speedup (or more) on a 75MB Q3 protXML file
(completed in 2 minutes 53 seconds, formerly gave up on it after a full
week of processing.)
o Improvement to XML parsing
o And various other bug fixes.
For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
For downloading the sourcecode please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
Thanks for your continued use, support, and feedback!
The SPC Tools team: Luis, David, Josh
jtasman
The cygwin distribution has been updated with a very small bug fix. The new cygwin package is ISB-MS-Tools-3.2-0b and will be reinstalled simply by rerunning the TPP_Cygwin_setup.exe installer program.
For those interested, the system would become confused if input and output filenames were similar.
Linux users, please update
/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx
from CVS source.
The SPC Tools team: Luis, David, Josh
Joshua Tasman
Dear SPC Tools Users,
We are releasing the next revision of the Trans-Proteomic Pipeline,
version 3.2.1 - SQUALL (cygwin package ISB-MS-Tools-3.2-1b). This
update includes the following changes and improvements:
o) X!Tandem with K-Score plugin is now included as a cygwin binary.
While we are still refining the PeptideProphet modeling of tandem
results, this should allow early adopters to play via the command-line,
and brings us close to providing a completely open-source, free,
proteomics solution! Source can be included by selecting the source
package under "Proteomics".
o) Pep3D
1) improves to interface: links are only generated if showing one
mzXML file (otherwise there is serious potential of returning an
enormous html file when multiple mzXML files in same analysis, esp.
from high-res intruments)
2) Minor changes to input form elements: Changed text for 'resolution'
and 'size' for clarity
o) Important fix to ASAPRatio results browser (fixing occasional
crashes/missing data display)
o) Fix to xinteract, which would have become confused if input and
output names were similar
and various other bug fixes.
=> For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
=> For downloading the sourcecode please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
=> Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
Joshua Tasman
Dear SPC Tools Users,
We are releasing the next revision of the Trans-Proteomic Pipeline,
version 3.2.2 - SQUALL (cygwin package ISB-MS-Tools-3.2-2d). This
update includes many changes and improvements and all users are
recommended to update their software.
NOTE: Cygwin users, please download and save the TPP_Cygwin_Setup.exe
program. Usually this does not need to be re-downloaded when the TPP is
updated, but the setup program itself has been updated to version 2.578.
http://tools.proteomecenter.org/software/TPP_Cygwin_Setup.exe
Some of the changes in the TPP 3.2.2 release include:
o) X!Tandem (with K-Score plugin): Cygwin distribution now contained
standard-named "tandem.exe". Linux source tree includes tandem source.
o) Tandem2XML: fixes for n-terminal modifications, and modifications
with greater than 3 digits left of the decimal point.
o) new program: Sqt2XML: converts SQT files into pepxml suitable for
searching with the TPP. Contributed by our new TPP developer Matt
Chambers-- thanks, Matt!
and many other bug fixes.
=> For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
=> For downloading the sourcecode please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
=> Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
The SPC Tools team: Josh, David, Luis
Joshua Tasman
The TPP has been updated to correct the missing ProteinProphet protein
annotation issue (cygwin package ISB-MS-Tools-3.2-2e). Linux users may
update source from
http://sashimi.svn.sourceforge.net/svnroot/sashimi/branches/release_3-2-2
Josh
Joshua Tasman
We are releasing the next revision of the Trans-Proteomic Pipeline,
version 3.3.0 - SQUALL (cygwin package ISB-MS-Tools-3.3-0b). This
update includes many changes and improvements and all users are
recommended to update their software.
Some of the exciting changes in the TPP 3.3.0 release include:
o) The X!Tandem (with K-Score plugin) search engine is now integrated
into Petunia (the TPP GUI) to make using this open-source search engine
even easier; ISB/SPC default parameter files are installated;
o) PeptideProphet: addition of new retention-time model; updates to the
accurate mass and pI models; bugfix to deal with negative distributions;
o) ProteinProphet: correction to references multiple source input files;
fix to protein annotations;
o) Xpress: fix to apply fixed scan ranges to elution peaks from
command-line options;
o) Sqt2XML: fixed bug which duplicated first protein as alternative
protein; fixed search engine name: defaults to "SEQUEST", but will
override with "SQTGenerator" header entry; no longer writes
search_result element for a spectrum_query with no hits.
For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
Joshua Tasman
There is a bug in the TPP v3.3.0 Cygwin installation involving the
gnuplot graphics package. Users are advised to avoid a clean install
until this is resolved tomorrow morning. Linux users are unaffected.
Apologies for the inconvenience,
Josh
Joshua Tasman wrote:
> Dear SPC Tools Users,
>
> We are releasing the next revision of the Trans-Proteomic Pipeline,
> version 3.3.0 - SQUALL (cygwin package ISB-MS-Tools-3.3-0b). This
> update includes many changes and improvements and all users are
> recommended to update their software.
>
> Some of the exciting changes in the TPP 3.3.0 release include:
>
> o) The X!Tandem (with K-Score plugin) search engine is now integrated
> into Petunia (the TPP GUI) to make using this open-source search engine
> even easier; ISB/SPC default parameter files are installated;
>
> o) PeptideProphet: addition of new retention-time model; updates to the
> accurate mass and pI models; bugfix to deal with negative distributions;
>
> o) ProteinProphet: correction to references multiple source input files;
> fix to protein annotations;
>
> o) Xpress: fix to apply fixed scan ranges to elution peaks from
> command-line options;
>
> o) Sqt2XML: fixed bug which duplicated first protein as alternative
> protein; fixed search engine name: defaults to "SEQUEST", but will
> override with "SQTGenerator" header entry; no longer writes
> search_result element for a spectrum_query with no hits.
>
>
> For downloading and installing the Windows version please visit the
> following guide on our wiki:
> "http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
>
> For downloading the source code, please go to the following link:
> "http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
>
> Everyone is encouraged to read and contribute to our wiki, at
> http://tools.proteomecenter.org/wiki/
>
>
Joshua Tasman
A new TPP cygwin release, version 3.3.0c, resolves the recent graphics issues some of you may have
been experiencing. Please rerun the installer; Base->ISB-MS-Tools and Graphics->gnuplot should both
automatically update.
(This release also fixes an issue with webserver configuration related to the new retention time model.)
Linux users, please note that the svn release branch has been updated; if you compile from svn
source you'll want to make sure your version of gnuplot is updated to 4.2.
Please let us know of any graphics issues you encounter.
Thanks,
Josh, David, Luis
Joshua Tasman wrote:
> Dear SPC Tools Users,
>
> We are releasing the next revision of the Trans-Proteomic Pipeline,
> version 3.3.0 - SQUALL (cygwin package ISB-MS-Tools-3.3-0b). This
> update includes many changes and improvements and all users are
> recommended to update their software.
>
> Some of the exciting changes in the TPP 3.3.0 release include:
>
> o) The X!Tandem (with K-Score plugin) search engine is now integrated
> into Petunia (the TPP GUI) to make using this open-source search engine
> even easier; ISB/SPC default parameter files are installated;
>
> o) PeptideProphet: addition of new retention-time model; updates to the
> accurate mass and pI models; bugfix to deal with negative distributions;
>
> o) ProteinProphet: correction to references multiple source input files;
> fix to protein annotations;
>
> o) Xpress: fix to apply fixed scan ranges to elution peaks from
> command-line options;
>
> o) Sqt2XML: fixed bug which duplicated first protein as alternative
> protein; fixed search engine name: defaults to "SEQUEST", but will
> override with "SQTGenerator" header entry; no longer writes
> search_result element for a spectrum_query with no hits.
>
>
> For downloading and installing the Windows version please visit the
> following guide on our wiki:
> "http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
>
> For downloading the source code, please go to the following link:
> "http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
>
> Everyone is encouraged to read and contribute to our wiki, at
> http://tools.proteomecenter.org/wiki/
>
>
jtasman
An update to TPP version 3.3.0 for cygwin has been released: package
3.3.0d. This update should resolve the recent issues some of you may
have been experiencing with an unexpectedly large number of peptides or
proteins. Please rerun the installer; Base->ISB-MS-Tools should
automatically update to version 3.3.0d.
Linux users, please update from the SVN release_3-3-0 TPP branch.
Thanks,
Josh, David, Luis
Joshua Tasman wrote:
> Dear SPC Tools Users,
>
> We are releasing the next revision of the Trans-Proteomic Pipeline,
> version 3.3.0 - SQUALL (cygwin package ISB-MS-Tools-3.3-0b). This
> update includes many changes and improvements and all users are
> recommended to update their software.
>
> Some of the exciting changes in the TPP 3.3.0 release include:
>
> o) The X!Tandem (with K-Score plugin) search engine is now integrated
> into Petunia (the TPP GUI) to make using this open-source search engine
> even easier; ISB/SPC default parameter files are installated;
>
> o) PeptideProphet: addition of new retention-time model; updates to the
> accurate mass and pI models; bugfix to deal with negative distributions;
>
> o) ProteinProphet: correction to references multiple source input files;
> fix to protein annotations;
>
> o) Xpress: fix to apply fixed scan ranges to elution peaks from
> command-line options;
>
> o) Sqt2XML: fixed bug which duplicated first protein as alternative
> protein; fixed search engine name: defaults to "SEQUEST", but will
> override with "SQTGenerator" header entry; no longer writes
> search_result element for a spectrum_query with no hits.
>
>
> For downloading and installing the Windows version please visit the
> following guide on our wiki:
> "http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
>
> For downloading the source code, please go to the following link:
> "http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
>
> Everyone is encouraged to read and contribute to our wiki, at
> http://tools.proteomecenter.org/wiki/
>
>
Joshua Tasman
Dear SPC Tools Users,
We are releasing the next revision of the Trans-Proteomic Pipeline,
version 3.4.0 (cygwin package ISB-MS-Tools-3.4-0a). This
update includes many changes and improvements and all users are
recommended to update their software.
Note that this is the beginning of the 3.4.x series. See below ("new TPP
version numbering scheme") for more information.
Some significant changes that all users should be aware of:
o) based on user feedback and extensive testing from our collaborators at
LabKey, major changes to the prophet models have been implemented, including
improved behavior in cases in which a model was not reported in 3.3.0. Users
who saw negative changes in 3.3.0 should see improved results. See below for
more information.
o) Out2XML officially replaces out2summary and sequest2xml: this allows for
direct conversion of Sequest .out files to pepXML files. The older programs are
still included to allow users time to transition to the new system, but will be
removed in the next major release (3.5.0)
o) MzXML2Search officially replaced by MsXML2Other: MsXML2Other is no longer
distributed or supported.
o) runProphet script retired: this was an older wrapper around ProteinProphet
and has been retired. Command-line users should use ProteinProphet directly, or
xinteract.
o) new TPP version numbering scheme: 3.4.0 introduces a new numbering scheme.
.1 (minor) increments will introduce new features, while 0.0.1 increments will
denote any bug fixes that change results. Cygwin packages ('a', 'b', etc) will
only be updates for cygwin-only fixes (to the webserver, etc.)
other important changes:
o) PeptideProphet:
- important fixes to binning which should restore performance
- Nonparametric modeling
- optional 'ignore charge'
- optional 'force model' option to proceed even under bad distribution
separation cases
o) ProteinProphet:
- fixes for NSP model used when dynamic NSP model has too few bins
o) runsearch: uses Out2XML instead of retired out2summary
o) xinteract:
- Added -F (force the fitting of the mixture model),
-P (non-parametric model), and
-IX (Ignore Charge States) options for xinteract;
o) Petunia:
- Added Metabolic and Fixed Scan Range options for Xpress;
- Merge dynamic parameters into tandem xml input into new file, instead of
forcing users to use large-format parameters file as input;
- Allow users to choose a directory in File Chooser;
- Display current directory in tree view (File Browser);
- Feed dta2mzxml a directory/*.dta as input (to avoid extremely long input
arguments);
- Added -byname option for dta2mzxml;
- Replaced Sequest2XML with Out2XML in GUI-initiated processing
- Removed msxml2other from GUI
- Minor text and layout fixes.
- Re-added Maldi and Mass options for Out2XML; Updated Enzyme list drop-down
- Retire runprophet; call ProteinProphet directly
For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-4-0
Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
The SPC Tools team: David, Luis, Josh
Joshua Tasman
We are releasing the next revision of the Trans-Proteomic Pipeline,
version 3.5.1 (cygwin package ISB-MS-Tools-3.5-1a). This
update includes many changes and improvements and all users are
recommended to update their software.
Note that this is the beginning of the 3.5.x series. (3.5.0 was an internal-only release.)
Some significant changes that all users should be aware of:
=TPP Version 3.5.0 Changes=
*significant PeptideProphet bug fixes and changes
*ASAPRatio: major bug fix
*file extension changes to .pep.xml and .prot.xml
*performance enhancements
*temporary TPP files cleaned up
*Tandem2XML
*xinteract: new prob 0 setting
*ProteinProphet: protein description reformatting
*Mascot2XML: parser fix
*major converter updates for ReAdW, wolf; introducing mzWiff (mzStar retired)
==significant PeptideProphet bug fixes and changes==
--bug fixes to allow modeling of ProbID using semi-supervised and semi-parameteric models
--bug fixes to allow semi-parameteric model to work with the force distribution and ignore charge options
--bug fix to correct computation of semi-parameteric model attributes (mean and stddev)
--bug fix to use the correct prior that includes the decoys when the DECOYPROBS option is used (ADVANCED OPTION: Use to test accuracy of program but not for final result reporting as selecting this option can make the probabilities inaccurate since it forces the program to assume that decoy matches are unknown when the final probabilities are calculated)
--(Re-)added max reward capping into PeptideProphet
=ASAPRatio: major bug fix==
ASAPRatioPeptideParser has been updated to correct an important bug: the previous version used modification masses specified in the pepXML file (which are average masses when fragment mass is selected to be average in the sequest.params file.) For high-mass accuracy instruments, where the monoisotopic mass should be used as the parent mass in the search parameters, ASAPRatio was ignoring the monoisotopic mass if specified on the command-line.
The updated version will correctly use the mass specified on the command-line. The command-line mass should be specified as the total monoisotopic mass of the modified amino acid(s).
This only affects high-mass-accuracy users who want to use a small window around the monoisotopic peak to detect the signal. If using default ASAPRatio parameters, this probably won't be an issue.
=file extension changes to .pep.xml and .prot.xml=
The default pepXML and protXML filename extensions are now “.pep.xml” and “.prot.xml” respectively, although older-style “.xml” and “-prot.xml” conventions still work seamlessly as input filenames. The existing commandline conventions for selecting output filenames are still there.
==performance enchancements==
Insilicos has folded in various performance enhancements from their retired IPP build of the sashimi tools.
==temporary TPP files cleaned up==
Tempfiles now all use generated unique names, so collisions between users should not be a problem (this was largely the case already, but not completely so).
CGI programs no longer leave temporary image files sitting around, they are deleted as soon as they are viewed. Also CGIs no longer try to clean up from previous runs by just deleting “*.png”.
==Tandem2XML==
Fix Tandem2XML to generate valid pepXML, even when "output, spectra" == "no". Turns out forcing this parameter yields something like 4x larger X! Tandem output, and it is killing the FHCRC. Also turns out, it is not that hard to fix.
6-digit precision for double values in Tandem2XML.
==xinteract: new prob 0 setting==
Fix xinteract to allow users to set prophet probability = 0 for both PeptideProphet and ProteinProphet.
==ProteinProphet: protein description reformatting==
The protein description string is written into protXML with spaces instead of pipes (vertical bars) in order
to make the HTML output tables less wide (and readable!)
==Mascot2XML parser fix==
Fixed parser error for modification data to consider parenthesis in name
==major converter updates for ReAdW, wolf; introducing mzWiff (mzStar retired)==
The official versions of ReAdW and wolf have been updated to version 3.5.1 with many changes.
mzWiff is a replacement for mzStar, and is much faster, more stable, and has more options.
Options for each converter can be found by running the programs with no arguments.
For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-5-1
Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
The SPC Tools team: Josh, Luis, David
Joshua Tasman
Dear SPC Tools Users,
We are releasing the next revision of the Trans-Proteomic Pipeline,
=TPP Version 3.5.0 Changes=
=ASAPRatio: major bug fix==
For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-5-1
Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
Joshua Tasman
Sorry for the inconvenience,
Josh
Joshua Tasman
Josh
jtasman
The Trans-Proteomic Pipeline 3.5.x series has been updated with the
release of version 3.5.2 (cygwin package ISB-MS-Tools-3.5-2a). This
update includes many changes and improvements and all 3.5.x users are
encouraged to update.
=TPP Version 3.5.2 Changes=
*converters: memory leak fixes corrected
ReAdW, wolf, and mzWiff had memory leaks that could accumulate if run
many times on the same machine. Special thanks to Dmitrii Tchekhovskoi
to catching and patching these bugs
*ReAdW and wolf: stricter options checking
The programs now correctly catch mis-formed arguments
*ReAdW: handling TSQ MRM data
*Mascot2XML: fix to handle yet another scan number description variant
("ScanNumber=xxx")
*Tandem2XML: as this program no longer processes MGF search results,
warn instead of error when mzXML file not found.
*calctppstat.pl: this helpful script which generates statistics on TPP
results has been updated (found in TPP/testing in source code.)
For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-5-2
Please refer to the readme file in TPP/src as well as the wiki.
Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
Joshua Tasman
For those who have yet to install 3.5.2, we will release another update in the near future (within the next 24 hours), so you might want to hold off.
Apologies for any inconvenience for the early adopters,
Josh
Joshua Tasman
Dear SPC Tools Users,
The Trans-Proteomic Pipeline 3.5.x series has been updated with the
release of version 3.5.3 (cygwin package ISB-MS-Tools-3.5-3a). All 3.5.x users are
encouraged to update.
=TPP Version 3.5.3 Changes=
==mzWiff==
1. Extends option -PI and -PP to accept an upper bound on intensity to be reported for tandem MS. (-PI<num1>-<num2> and -PP<num1>-<num2>)
2. Added option -P1I and -P1P to accept an upper bound on intensity to be reported for MS1.
3. Perform low level format processing to retrieve creator software and version. (Some reports that older Analyst(QS) library fails to acquire this information from file written by new Analyst(QS) version.)
4. Perform low level format processing to determine if an associated external scan file (.wiff.scan) is used and check for it existence. (Numerous reports of user not providing .wiff.scan file)
5. Added option --showwifftree which will print out the storage structure of a wiff file and all the textual string in the first 512 bytes. (Purely for debugging.)
==ramp==
ramp is the mzXML parsing code underlying all mzXML-processing components of the TPP.
* a couple of changes to fix infinite loop behavior in XPressCGI when the needed mzXML file has been removed
* memory leak fixed
* wasn't reading mzData collisionEnergy (Thanks to contributor Paul Benton)
* mzData precursorIntensity, was reading as int instead of double
* tweak for to build standalone (non-TPPlib) RAMP under MSVC compiler
==Out2XML==
* now exits with meaningful error message when encountering an empty out file, indicating an incomplete sequest run.
==plot-msms==
* added support for MS3 scans; will plot them now and also plot out corresponding full MS2 scan in the precursor area
==XPress Peptide Viewer==
* writes maximum intensity value at left of plot; previously value was being cutoff on top-right of plot
* will not change printed maximum intensity value when the "Norm" option is checked
* increase tol and z input textbox sizes; size=1 apparently renders too small in Safari
==All converters (mzWiff, ReAdW, wolf)==
* Correction to mzXML output: writes "Full" instead of "FULL" (thanks to Rune Schjellerup Philosof)
==temp images files==
* path issue fix.
For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-5-3
Please refer to the readme file in TPP/src as well as the wiki.
Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
Josh T
use ASAPRatio, updating ASAPRatio results through the web interface
will *delete* the corresponding pepXML file.
Please check any files you have tried to update in the recent past.
An update will be made as soon as this is resolved.
-Josh
On Apr 14, 9:16 pm, jtasman <jtas...@systemsbiology.org> wrote:
> Dear SPC Tools Users,
>
> The Trans-Proteomic Pipeline 3.5.x series has been updated with the
> release of version 3.5.2 (cygwin package ISB-MS-Tools-3.5-2a). This
> update includes many changes and improvements and all 3.5.x users are
> encouraged to update.
>
> =TPP Version 3.5.2 Changes=
>
> *converters: memory leak fixes corrected
> ReAdW, wolf, and mzWiff had memory leaks that could accumulate if run
> many times on the same machine. Special thanks to Dmitrii Tchekhovskoi
> to catching and patching these bugs
>
> *ReAdW and wolf: stricter options checking
> The programs now correctly catch mis-formed arguments
>
> *ReAdW: handling TSQ MRM data
>
> *Mascot2XML: fix to handle yet another scan number description variant
> ("ScanNumber=xxx")
>
> *Tandem2XML: as this program no longer processes MGF search results,
> warn instead of error when mzXML file not found.
>
> *calctppstat.pl: this helpful script which generates statistics on TPP
> results has been updated (found in TPP/testing in source code.)
>
> For downloading and installing the Windows version please visit the
> following guide on our wiki:
> For downloading the source code, please go to the following link:
> or directly from svn: seehttp://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-5-2
>
Brian Pratt
environment variable for your webserver, *and* it specifies a directory for
your tempfiles which is on a different volume than your result files. So
for pretty much everyone using TPP this is a non-event.
- Brian
Joshua Tasman
Josh
Joshua Tasman
Dear SPC Tools Users,
The Trans-Proteomic Pipeline 3.5.x series has been updated with the
release of version 3.5.4 (cygwin package ISB-MS-Tools-3.5-4a). All 3.5.x users are
encouraged to update.
=TPP Version 3.5.4 changes (since 3.5.3)=
* IMPORTANT NOTE: converter binaries are not distributed in this version. Please download them directly from SourceForge (see links below). Please remember, you must run the vcredist_x86.exe program one time, before running the converters.
==new ProteinProphet options==
new command-line options: PROTLEN (calculates protein length and reports it in protXML), NORMPROTLEN (normalizes NSP by protein length; previously PROTLEN param), PROTMW (calculates protein molecular weight from the database and reports it in protXML).
==temp files==
improved handling for temporary files throughout the TPP
==Mascot2XML==
Another fix to Mascot2XML to handle "Scan Number: nnn" variant of scan title, appearing in some Mascot files.
==converters(ReAdW, wolf, mzWiff)==
* minor bug fixed in experimental mzML output: base peak m/z and intensity values had been reversed.
For downloading and installing the Windows version please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_3-5-4
Please refer to the readme file in TPP/src as well as the wiki.
Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
The SPC Tools team: Josh, David, Luis
Joshua Tasman
-Josh