TPP:5.0.0 Release Notes

From SPCTools

(Difference between revisions)

Revision as of 20:07, 30 August 2016

Trans-Proteomic Pipeline (TPP) software, release 5.0.0 is a major release of TPP that contains new features, improvements, and fixes to 4.8.0. The software is available for Windows as well as Linux (and unofficially) for OSX from all the usual locations (please see the section below, "Getting the software"). Most users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a web server). For advanced users who need to customize the TPP, or for those who run on Linux or OS X, you can download the source code. Again, most users don't need build from source, and should use the Windows installer.

Previous release notes are available at TPP:4.8.0_Release_Notes

1 Major Changes and Overview
2 New Features
3 Improvements/Changes
4 Bug fixes
5 Miscellaneous
6 Known Issues
7 Getting the TPP Software
8 Acknowledgements
9 SVN Log

Major Changes and Overview

Heavily modified and streamlined code organization, build, and installation system

64-bit

Windows installer:
- includes all external dependencies, including stand-alone Apache web server (uses port 10401, user configurable), Strawberry perl, and ProteoWizard (via its own installer)
- allows for user-configurable software and data locations
- new (optional) TPP Tray application provides convenient shortcuts to TPP, web server control, and data and log folders

New major software components:
- Kojak for cross-linking analysis
- DISCO for analysis of DIA data without using spectral libraries
- StPeter for label-free protein quantitation via MS2 normalized spectral indices

Updated user interface look and feel

More details below.

New Features

New PeptideMapper tool???

PepxMLViewer:
- Link iProphet prob to new models page
- Added iProphet quick-filter to summary section
- Moved iProphet probability to first column by default
- Added filter options for all iProphet models and cleaned up options
- Removed obsolete iProphet fields from possible column list
- Added support for cross-linking results (specifically from Kojak):
  - display both peptides and both proteins from 'xl' entries, along with their individual scores and overall spectrum search scores
  - link to (tabbed) Lorikeet with both peptides
  - Added filter options for KOJAK fields
  - Includes support for PLink and ProteinProspector cross-link results
- Display "KScore" as the column heading when viewing XTandem K-score results (stored in pepXML as "hyperscore")
- Pass ions series from search params to Lorikeet
- Changed column headers: "ions"-->"ions_old" (old viewer), "ions2"-->"ions" (lorikeet)
- Allow NTT filter to have min and max values; also added similar filter for NMC
- Clean up alignment of various filters and options
- Expanded size of filename text box
- Clean up display for quantitation fields and less popular search engines (Myrimatch, OMSSA, MSGF+, etc).
- Added ability to format unruly values into decimal or scientific notation

ProteinProphet:
- Generate error vs min_prob table and insert into protXML (similar to the one produced by PeptideProphet)
- Write sens/error info into XML by ascending error rate (as in the other prophets)
- Stop plotting sens/err png by default; removed NOPLOT option. To produce png, use new PLOTPNG option.
- New progress bars and cleaner, more consistent user feedback

PTMProphet
- Added ability to look for neutral loss ions (new command-line spec)
- User-defined MS2 tolerance (PPMTOL)
- MINPROB parameter to ignore low scoring spectra

Petunia:
- Extensive Look&Feel revamp:
  - simplified and streamlined navigation and menus
  - new style for tools sections and submit buttons
  - Animate button after action is submitted until completion (e.g. Copy/Paste a large file)
  - highlight selected checkboxes and radio buttons for clarity
  - darkened body background
  - added dynamic filter to Speclibs page
  - Updated menu names, tool descriptions, and tooltips
  - Added 'filter files here' hint text to files filter box
  - added basic Comet and Kojak params editor page
    - inserts date/time and user info as a comment when saving comet/kojak params via Petunia
    - Added Comet and Kojak help link for each search parameter
  - Enhanced view jobs page:
    - Do not display full jobs list when viewing a specific command output
    - Do not display 'Kill Command' link in Jobs page once command is finished
    - Only display bubble with number of running/active jobs next to Jobs tab menu title (mouse-over still displays status summary of all jobs)
    - Add filter box on jobs page

- Add visual separator between current directory tree and list of subdirectories in filebrowser/picker

- - Spified up Mascot search page: add page size filter, highlight selected file to download, collapse server URL setting if results are returned
  - updated to current ISB logo
- Added interfaces to St.Peter, Kojak, DISCO, and RefreshParser
- Added Kojak to list of search engines ("pipeline type")
- Added simple interface to Percolator (if installed)
- Added Neutral Losses in PTMProphet page
- Added support for TMT-10 in Libra conditions page
- Only display m/z of relevant channels when selecting from drop-down in Libra conditions page; blank out all other channel masses
- Subtly highlight when running a sub-command in command output (e.g. as in xinteract)
- Fix calling Libra via ProteinProphet by including condition file name and cd to output dir
- Removed MaRiMba interface

tpp_models:
- Capture StPeter analysis values
- Display decoy-based ROC curves, with error bars
- Display new error table from protXML, if present
- Add run datetime; removed debug tab (still available in DEBUG mode)
- Do not display error tables tab if no data

Include Kojak 1.5.1 and related conf file

Updated to Comet 2016.01.2 and related params file

Updated to latest Lorikeet (Sept.2015)

Addition of hardklor to support DISCO

New versions of pepXML and protXML schemae

Improvements/Changes

InteractParser:
- Add option to record ion_injection_time in pepXML

ASAPRatio:
- Write xml-compliant 'NaN' string when applicable
- Removed obsolete .bof files code
- Added progress bar
- Display executable name and version at launch

PTMProphet:
- auto-populate modifications not known to SpectraST Peptide library

PeptideProphet:
- Expanded N-Glyc model
- Expanded mass models to allow for search offsets

ProteinProphet:
- Warn users if protein has any zero-mass residues, and display them with affected sequence
- Fix call to Libra (use condition file, not channel number)
- Updated and reformatted usage statement

RespectParser:
- New options to remove peaks (instead of attenuate) and for output file suffix

Libra
- Boosted performance of protein ratio calculation by 100x or more by doing a single pass over source pepXML files
- Use higher precision for channels in order to support TMT-10 tags
- Added progress bar
- Record version in XML file after analysis

Petunia
- Use Digest::MD5 to calculate md5 checksum instead of system call

ProtXMLViewer:
- Added support for StPeter quantitation results
- Added ability to sort peptides
- View quant ratios as either numerical (with errors) or graphical bars
- Added basic spectrum stats for XPRESS results
- Show peptide map graphic when viewing shared peptides via the weight link
- Add peptides to exported TSV results and provide link to open directly (change default file extension to .tsv)

Sequence viewer:
- Attempt to map peptides via I/L substitution when first pass fails

Spectrum Viewer:
- Scale all spectra to 0 < mz < 2000 unless more data present (eases comparison of spectra)
- Handle fragment mass error and pass it to Lorikeet
- Added ability to view up to 5 interpretations of a single spectrum in same window via js tabs, with customizable labels and animation control
- Also used for visualization of cross-linked peptide results

Comet hits viewer
- Added support for cases when mz data file is in different directory than pepXML file
- Updated link to Lorikeet by passing mzML file, scan number, and charge
- Added link to view top 5 hits in the updated spectrum viewer
- Added page title and html footer with TPP version

SpectraST
- Multi-threaded search
- Added selenium-related modifications
- Glyco-peptide support
- Include standard iRT values; extract RT from mzML if not in pepXML
- Use Lorikeet to view spectra
- Look for spectrast.usermods in splib's directory

RTCatalog:
- updated with more features

Bug fixes

Fixed definition for lysn_promisc enzyme (to [X]|[KR])

InteractParser:
- Do not crash when protein descriptions are blank
- Upgrade scan numbers to long
- Fix instances where 'scan=' is not found within nativeSpectrumID
- fix spetrum name mangling under certain nativeSpectrumID conditions
- Fix recording of variable mods if they were not listed in order in source pepXML

PTMProphet
- Fixed memory leak

PepXMLViewer:
- regenerate index when a new column is added, and keep the column always in display
- corrected issue with bad byte offsets in large files

ProteinProphet:
- Synced usage statement, removed obsolete XML option
- Fixed computation of protein lengths
- Check for existence of input files before attempting to open them; provide meaningful feedback to user

Spectrum Viewer:
- Faster rendering of spectra from MS2-only files

Comet hits viewer
- Fixed bug where bad comparison of mass_type ("average") strings resulted in incorrect url param

ProtXMLViewer:
- Fix sorting for very large sub-groups (that go past az)

CompareProts:
- Fix display of mouseovers in 2-list protein comparison

SpectraST
- Corrected proton mass

Mascot2XML
- Fix mass error due to differing masses for proton

Tandem2XML
- Corrections to modifications problems when using lots of mods

Miscellaneous

Major code reorganization and standardization:
- Updated path furnishing utilities, as some paths are user-settable post-compilation
- Renamed all ".cxx" C++ source files as ".cpp"
- Harmonize directory names
- Moved Enzyme code to Common/
- moved COVERAGE/ folder into src/Util and renamed it batchcoverage (its target name)
- Moved xtandem out of extern/ and into src/Search
- Updated boost

Removed no longer needed or supported components:
- refresh_interact, runperl, run_in
- Visual Studio project files
- Misc .bat files.
- fdr_plot.cpp, getSpectrum.cpp, mzxml2dta1.cpp, plottic1.cpp, prophet_png1.cpp, tryp_model.txt
- Old help files
- Outdated database download scripts
- Cygwin-related code and settings

Using Inno to produce Windows installer

Known Issues

Kojak graphical models in PeptideProphet are not displaying correctly on the MODELS page.
Peptides with multiple PTMProphet results will only display one type of mod in PepXMLViewer (due to last minute schema change)

Getting the TPP Software

Download the TPP version 5.0.0 native windows installer (TPP_Setup_v5_0_0.exe) from the Sashimi SourceForge project file release page:

 http://sourceforge.net/projects/sashimi/files/

Everyone is encouraged to read and contribute to our wiki, at

 http://tools.proteomecenter.org/wiki/

For guides to installing and using our software, please see our wiki:

 http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP

For downloading the source code, please go to the following link:

 http://sourceforge.net/projects/sashimi/files/ and find the 5.0.0 source code .tgz package;

Or, check out the code directly from svn:

 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_5-0-0

For building from source, please refer to the README and INSTALL files in src/ directory of TPP as well as this wiki.

Acknowledgements

The TPP Team: David, Luis, Mike, Jimmy, and our old colleague Joe, plus all other developers who contributed to this release from the ISB. Thanks to developers and users from the TPP's user community who provided feedback and code contributions.

SVN Log

The SVN log of all changes since the previous release are available at TPP:5.0.0_SVN_Log.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:5.0.0_Release_Notes"

 == Major Changes and Overview ==
-* Heavily modified code organization, build, and installation system
+* Heavily modified and streamlined code organization, build, and installation system
 * '''64-bit'''
 * Windows installer:
-** '''includes''' all external dependencies, including stand-alone '''Apache''' web server (uses port 10401, user configurable) and Strawberry '''perl'''
+** '''includes''' all external dependencies, including stand-alone '''Apache''' web server (uses port 10401, user configurable), Strawberry '''perl''', and '''ProteoWizard''' (via its own installer)
 ** allows for user-configurable software and data locations
 ** new (optional) TPP Tray application provides convenient shortcuts to TPP, web server control, and data and log folders
 * ''PepxMLViewer'':
 ** Link iProphet prob to new models page
+** Added iProphet quick-filter to summary section
+** Moved iProphet probability to first column by default
+** Added filter options for all iProphet models and cleaned up options
+** Removed obsolete iProphet fields from possible column list
+** Added support for cross-linking results (specifically from Kojak):
+*** display both peptides and both proteins from 'xl' entries, along with their individual scores and overall spectrum search scores
+*** link to (tabbed) Lorikeet with both peptides
+*** Added filter options for KOJAK fields
+*** Includes support for PLink and ProteinProspector cross-link results
+** Display "KScore" as the column heading when viewing XTandem K-score results (stored in pepXML as "hyperscore")
+** Pass ions series from search params to Lorikeet
+** Changed column headers: "ions"-->"ions_old" (old viewer), "ions2"-->"ions" (lorikeet)
+** Allow NTT filter to have min and max values; also added similar filter for NMC
+** Clean up alignment of various filters and options
+** Expanded size of filename text box
+** Clean up display for quantitation fields and less popular search engines (Myrimatch, OMSSA, MSGF+, etc).
+** Added ability to format unruly values into decimal or scientific notation
 * ''ProteinProphet:''
+** Generate error vs min_prob table and insert into protXML (similar to the one produced by PeptideProphet)
+** Write sens/error info into XML by ''ascending'' error rate (as in the other prophets)
+** Stop plotting sens/err png by default; removed NOPLOT option.  To produce png, use new PLOTPNG option.
+** New progress bars and cleaner, more consistent user feedback
 * ''PTMProphet''
 * ''Petunia:''
+** Extensive Look&Feel revamp:
+*** simplified and streamlined navigation and menus
+*** new style for tools sections and submit buttons
+*** Animate button after action is submitted until completion (e.g. Copy/Paste a large file)
+*** highlight selected checkboxes and radio buttons for clarity
+*** darkened body background
+*** added dynamic filter to Speclibs page
+*** Updated menu names, tool descriptions, and tooltips
+*** Added 'filter files here' hint text to files filter box
+*** added basic Comet and Kojak params editor page
+**** inserts date/time and user info as a comment when saving comet/kojak params via Petunia
+**** Added Comet and Kojak help link for each search parameter
+*** Enhanced view jobs page:
+**** Do not display full jobs list when viewing a specific command output
+**** Do not display 'Kill Command' link in Jobs page once command is finished
+**** Only display bubble with number of running/active jobs next to Jobs tab menu title (mouse-over still displays status summary of all jobs)
+**** Add filter box on jobs page
+- Add visual separator between current directory tree and list of subdirectories in filebrowser/picker
+*** Spified up Mascot search page: add page size filter, highlight selected file to download, collapse server URL setting if results are returned
+*** updated to current ISB logo
+** Added interfaces to St.Peter, Kojak, DISCO, and RefreshParser
+** Added Kojak to list of search engines ("pipeline type")
+** Added simple interface to Percolator (if installed)
+** Added Neutral Losses in PTMProphet page
+** Added support for TMT-10 in Libra conditions page
+** Only display m/z of relevant channels when selecting from drop-down in Libra conditions page; blank out all other channel masses
+** Subtly highlight when running a sub-command in command output (e.g. as in xinteract)
+** Fix calling Libra via ProteinProphet by including condition file name and cd to output dir
+** Removed MaRiMba interface
 * ''tpp_models:''
 ** Capture StPeter analysis values
-** Display decoy-based ROC curves, with errorbars
+** Display decoy-based ROC curves, with error bars
+** Display new error table from protXML, if present
+** Add run datetime; removed debug tab (still available in DEBUG mode)
+** Do not display error tables tab if no data
 * Include ''Kojak'' 1.5.1 and related conf file
 * Updated to ''Comet'' 2016.01.2 and related params file
-* Adding ''hardklor'' to support DISCO
+* Updated to latest ''Lorikeet'' (Sept.2015)
-* New versions of ''pepXML'' and ''protXML'' schemae.
+* Addition of ''hardklor'' to support DISCO
+* New versions of ''pepXML'' and ''protXML'' schemae
 ** Write xml-compliant 'NaN' string when applicable
 ** Removed obsolete .bof files code
+** Added progress bar
+** Display executable name and version at launch
 * ''PTMProphet'':
 * ''ProteinProphet'':
-** More user and progress feedback
+** Warn users if protein has any zero-mass residues, and display them with affected sequence
+** Fix call to Libra (use condition file, not channel number)
+** Updated and reformatted usage statement
 * ''RespectParser'':
 *''Petunia''
 ** Use Digest::MD5 to calculate md5 checksum instead of system call
+* ''ProtXMLViewer'':
+** Added support for StPeter quantitation results
+** Added ability to sort peptides
+** View quant ratios as either numerical (with errors) or  graphical bars
+** Added basic spectrum stats for XPRESS results
+** Show peptide map graphic when viewing shared peptides via the weight link
+** Add peptides to exported TSV results and provide link to open directly (change default file extension to .tsv)
 * ''Sequence viewer'':
 * ''Spectrum Viewer'':
 ** Scale all spectra to 0 < mz < 2000 unless more data present (eases comparison of spectra)
-** Added ability to view up to 5 interpretations of a single spectrum in same window via js tabs, with animation control
+** Handle fragment mass error and pass it to Lorikeet
-** Added link from Comet hits to link to this page with top 5 hits
+** Added ability to view up to 5 interpretations of a single spectrum in same window via js tabs, with customizable labels and animation control
 ** Also used for visualization of cross-linked peptide results
 ** Added support for cases when mz data file is in different directory than pepXML file
 ** Updated link to Lorikeet by passing mzML file, scan number, and charge
+** Added link to view top 5 hits in the updated spectrum viewer
+** Added page title and html footer with TPP version
 * ''SpectraST''
 ** Added selenium-related modifications
 ** Glyco-peptide support
+** Include standard iRT values; extract RT from mzML if not in pepXML
+** Use Lorikeet to view spectra
+** Look for ''spectrast.usermods'' in splib's directory
+* ''RTCatalog'':
+** updated with more features
 ** Upgrade scan numbers to ''long''
 ** Fix instances where 'scan=' is not found within nativeSpectrumID
+** fix spetrum name mangling under certain nativeSpectrumID conditions
 ** Fix recording of variable mods if they were not listed in order in source pepXML
 ** Fixed memory leak
-* ''PepxMLViewer'':
+* ''PepXMLViewer'':
 ** regenerate index when a new column is added, and keep the column always in display
 ** corrected issue with bad byte offsets in large files
 * ''ProteinProphet'':
 ** Synced usage statement, removed obsolete XML option
+** Fixed  computation of protein lengths
 ** Check for existence of input files before attempting to open them; provide meaningful feedback to user
 * ''Spectrum Viewer'':
 ** Faster rendering of spectra from MS2-only files
+* ''Comet hits viewer''
+** Fixed bug where bad comparison of mass_type ("average") strings resulted in incorrect url param
+* ''ProtXMLViewer'':
+** Fix sorting for very large sub-groups (that go past ''az'')
+* ''CompareProts'':
+** Fix display of mouseovers in 2-list protein comparison
+* ''SpectraST''
+** Corrected proton mass
 * ''Mascot2XML''
 ** ''fdr_plot.cpp'', ''getSpectrum.cpp'', ''mzxml2dta1.cpp'', ''plottic1.cpp'', ''prophet_png1.cpp'', ''tryp_model.txt''
 ** Old help files
+** Outdated database download scripts
 ** Cygwin-related code and settings
 * ''Kojak'' graphical models in ''PeptideProphet'' are not displaying correctly on the MODELS page.
+* Peptides with multiple ''PTMProphet'' results will only display one type of mod in ''PepXMLViewer'' (due to last minute schema change)

TPP:5.0.0 Release Notes

From SPCTools

Revision as of 20:07, 30 August 2016

Contents

Major Changes and Overview

New Features

Improvements/Changes

Bug fixes

Miscellaneous

Known Issues

Getting the TPP Software

Acknowledgements

SVN Log

Views

Personal tools

Navigation

support newsgroups

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