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.)
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.c xx from CVS source.
> 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.)
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
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!
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
> 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!
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.
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.
> 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.
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.
> 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.
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.
> 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.
