TPP:5.2.0 Release Notes

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Revision as of 00:48, 22 December 2018

Trans-Proteomic Pipeline (TPP) software, release 5.2.0 is a major release of TPP that contains new features, improvements, and fixes to 5.1.0. 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.

For installation help, please see TPP:5.2_Installation.

Previous release notes are available at TPP:5.1.0_Release_Notes

1 Major Changes
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

Added basic integration of ProteinProspector results into TPP

Added compute_p, a new simple utility to compute p-values for some common distributions using GSL

New Features

InteractParser
- report TIC and S2N in pepXML

ProteinProphet
- Implement XPRESS_INT parameter to run XPressProteinRatioParser with new -i option
- Don't report raw_intensity when unavailable

Petunia
- Added support for reporting intensity-based ratios in XPRESS

PepXMLViewer
- Added (and fixed) support for XPRESS fields: light_area, heavy_area, light_intensity, heavy_intensity, intensity_ratio
- Added support for XPRESS label-free analysis; new fields are: peak_area (default), first_scan, last_scan, peak_intensity, peak_intensity_scan
- Implement background color gradient for intensity-based XPRESS ratios

ProtXMLViewer

XPRESS
- Implement calculation of protein ratios based on peptide peak intensities (new -i option in XPressProteinRatioParser)
- Added new "ratio_basis" attribute to protXML (possible values are "area" and "intensity")

DISCO

StPeter

Include comet 2018.01.3 and related conf file -- Please read the relevant Comet release notes, as some parameters have changed behavior
Include Kojak 1.5.5 and related conf file
Include ProteoWizard tools v3.0.10141 (3.0.11537 on Windows)
Updated versions of 'Lorikeet,...

Improvements/Changes

ProteinProphet
- compute exact error rates based on existing probabilities of all proteins (rather than applying artibtrary minimum probability thresholds)
- expand isotopic offsets considered for mass diff to -1,0,1,2,3 for Open Mass Searching

ProteoWizard
- set centroid CV term

PTMProphet
- auto enable DIRECT mode under specific conditions
- multi-threading
- other performance improvements
- Report processing progress in one line (overwriting itself), instead of creating a new one each time, to save space on output
- use the max of user set mz tolerance and PSM massdiff to localize
- make options to set N-term and C-term fragment ions for PTMProphet to consider

Disco
- Report number of precursors being tracked
- Improve code for tracking the precursors near their local peak maxima to improve efficiency
- Streamline parallel execution
- Remove RT in secs correction factor
- Upgrade threading to use c++11 standard library

RefreshParser
- Report number of _UNMAPPED entries

XPRESS
- Set default number of isotope peaks (-p) to "1"
- Added usage statement to XPressProteinRatioParser
- Establish a floor (0.001) and ceiling (999.0) for intensity-based peptide ratios (as is done for area-based ratios). Also report "-1" when no ratio can be calculated.
- Remove unsused -C option from XPressPeptideParser usage statement (and minor clean-up)
- Fix various memory leaks and minor code clean-up

Petunia
- Added option to run XPRESS label-free analysis
- Re-arranged XPRESS options for more logical/visual flow
- Remove StPeter option for exporting non-normalized results

PepXMLViewer
- Report number of *_UNMAPPED protein entries, when present, and disable links to sequence viewer from such entries
- Display list of search engines when viewing iProphet results
- Freshen up the help page to reflect current state of viewer, and clean up grammar/spelling
- Plot histograms with 1000 bins by default

ProtXMLViewer
- Attempt to guess organism from Uniprot annotations (OS=xxx yyy)
- Give breakdown of number of entries, single hits, spectra, etc by organism
- Update Gaggle format for export to Firegoose/Chrome Goose
- Added label when viewing intensity-based ratios from XPRESS

Spectrum Viewer
- Display Annotated Ion Current
- faster reading of spectra by use of index

xinteract
- Change meaning of -Ot option; it now will pass PLOTPNG option to ProteinProphet (replacing long-vacated NOPLOT option)

ShowXIC
- user settable MAXPPM error tolerance

tpp_models
- Added support for XPRESS label-free analysis parameters
- Capture and display Phospho models, when available

MzXML2Search
- take advantage of the index to faster read spectrum headers with mzParser

StPeter
- Changed how modifications are tracked and handled (no longer requires lookup table)
- Cosmetic changes to verbage during use.
- Removed exporting of non-normalized results and removed unintended creation of text files used during testing
- Use natural log fragment ion peak values

RTCatalog
- new option DISCO to allow building catalog from DISCO/DIAUmpire results
- Allow for negative RT values as some iRTs can be negative
- prevent overwriting existing files

madcaps
- Use case-sensitive option (-C) when calling subsetdb for faster performance (>100x faster with PEFF files!)
- Bolden keywords (KEY=) in protein annotations
- Provide direct link to neXtProt proteomics page for "nxp:NX_" entries
- Adjust width and alignment of sequence zoom window

subsetdb
- For case-insensitive searches, only apply toupper() to chars in the range a-z - this boosts performance by an order+ of magnitude when processing PEFF databases

Tandem2XML
- new options to allow it to work with newer versions of tandem and format spectrum names for TPP according to TPP conventions

SpectraST
- New function for returning the nearest peak to a given mz value in a spectrum

reSpect
- when multiple spectra of the same scan number are in the same analysis, only process the highest probability PSM

HardKlor
- allow modeling of intesities less than 1

indexmzXML
- New wrapper to run indexer, which renames .new file (if generated). Have Petunia call this instead of running the executable directly to avoid mis-communication to user when no .new file is created (i.e. index was good)

cramp
- use index for speed in reading peakLists

Bug Fixes

InteractParser
- Fix bug that mangled spectrum names from files that contain a dot in their names
- Fixed bad logic (from r6329) that prevented fallback capture of scans and charge from spectrum names
- Plug various memory leaks
- fix bug when processing filtered mzML files
- Apply -C (correct charge states) automatically for OMSSA files
- clean up usage statement and enzyme display

ProteinProphet
- Partial fixes for memory leaks, some code clean-up

PTMProphet
- neutral losses were not being picked up from the commandline nor utilized correctly

iProphet
- make use of spectrum_label when available

PTMProphet

StPeter
- Fixed bug that skipped n-terminally modified peptides

XPRESS
- fix logic for actually reporting intensity-based ratios when using -H or -L options
- fix typo in heavy_intensity_scan tag name

LibraPeptide

Mascot2XML
- More descriptive warning messages for poorly formatted Mascot results
- Allow conversion to proceed after reporting the issues

Petunia

PepXMLViewer

ProtXMLViewer

Spectrum Viewer

DISCO
- Fix file output of intermediate results on Windows

batchcoverage
- Fix memory leaks, clean up code

decoyModels

comet-fastadb

tpp_models

PeptideProphet
- tell Mascot user which scores are missing
- SpectraST modeling correct errors in initial settings

subsetdb
- fix parsing non-matching strings into correct variable
- Bump buffer to 500k bytes to accommodate super long PEFF description lines (longest so far observed is 210k chars!)

Enzymes
- Adding alternative enzyme names and fixing incorrect expression for TrypChymo

updatepaths
- Ensure new directory is an absolute path
- Make sure we are updating the desired attribute's value (and not some other matching string within the tag)
- Perform extension-free check only if original file name is not found (fixes case when pepXML reference files within a protXML file got mismapped like so: interact.pep.xml --> interact.prot.xml)
- Remove duplicated documentation

mzParser
- fix bug associated with reading scan headers using the scan index, for files that are filtered for a subset of scans

Apache/conf

Miscellaneous

Compilation/build
- Fix mingw compilation issue of tandem
- Enable SIMD in tandem code to compile under MINGW gcc
- Enable -std=c++11 for sufficiently high versions of gcc
- compile InteractParser with gsl for stats
- changes to compile on RedHat OS7 gcc 4.8.2
- Use std::isnan to allow pwiz to compile, include <cmath>
- Adding back protovis which is utilized in RTCatalog for drawing RT gradient corrections page
- Fix problem with windows build not copying the pwiz msi to the staging area
- Fix runtime bug with using boost regex match extra flag ... was crashing PepXMLViewer

ProtXMLViewer
- Reduced size of font for entry id

Removed all references to cygpath -- the first of several steps to remove long-unmaintained and deprecated cygwin code
Removed all references to WINDOWS_CYGWIN -- the second step...
Removed several old, deprecated cgis and references to them (mostly old ProtXMLViewer helpers), and other unused code

Known Issues

Getting the TPP Software

Download the TPP version 5.2.0 native windows installer (TPP_Setup_5.2.0.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 5.2.0 source code .tgz package

Or, check out the code directly from svn:

 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_5-2-0

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, Eric, Jimmy, plus all other developers who contributed to this release from 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 is available at TPP:5.2.0_SVN_Log.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:5.2.0_Release_Notes"

 * Added basic integration of '''ProteinProspector''' results into TPP
+* Added '''compute_p''', a new simple utility to compute p-values for some common distributions using GSL
 = New Features =
-* ''PeptideProphet''
+* ''InteractParser''
-**
+** report TIC and S2N in pepXML
 * ''ProteinProphet''
 ** expand isotopic offsets considered for mass diff to -1,0,1,2,3 for Open Mass Searching
-* ''SpectraST''
+* ''ProteoWizard''
-**
+** set centroid CV term
 * ''PTMProphet''
 ** other performance improvements
 ** Report processing progress in one line (overwriting itself), instead of creating a new one each time, to save space on output
+** use the max of user set mz tolerance and PSM massdiff to localize
+** make options to set N-term and C-term fragment ions for PTMProphet to consider
 * ''Disco''
 ** Display list of search engines when viewing iProphet results
 ** Freshen up the help page to reflect current state of viewer, and clean up grammar/spelling
+** Plot histograms with 1000 bins by default
 * ''ProtXMLViewer''
 * ''Spectrum Viewer''
-**
+** Display Annotated Ion Current
+** faster reading of spectra by use of index
 * ''xinteract''
 ** Change meaning of -Ot option; it now will pass PLOTPNG option to ProteinProphet (replacing long-vacated NOPLOT option)
-* ''Pep3D''
+* ''ShowXIC''
-**
+** user settable MAXPPM error tolerance
 * ''tpp_models''
 ** Added support for XPRESS label-free analysis parameters
+** Capture and display Phospho models, when available
-* ''ProteoGrapher''
+* ''MzXML2Search''
-**
+** take advantage of the index to faster read spectrum headers with mzParser
 * ''StPeter''
 * ''RTCatalog''
-**
+** new option DISCO to allow building catalog from DISCO/DIAUmpire results
+** Allow for negative RT values as some iRTs can be negative
+** prevent overwriting existing files
 * ''madcaps''
 ** For case-insensitive searches, only apply toupper() to chars in the range a-z - this boosts performance by an order+ of magnitude when processing PEFF databases
-* ''digestdb''
+* ''Tandem2XML''
-**
+** new options to allow it to work with newer versions of tandem and format spectrum names for TPP according to TPP conventions
-* ''readmzXML''
+* ''SpectraST''
-**
+** New function for returning the nearest peak to a given mz value in a spectrum
-* ''mzParser''
+* ''reSpect''
-**
+** when multiple spectra of the same scan number are in the same analysis, only process the highest probability PSM
-* ''pepXML schema'' v1.22
+* ''HardKlor''
-**
+** allow modeling of intesities less than 1
-* Windows Installer
+* ''indexmzXML''
-**
+** New wrapper to run indexer, which renames .new file (if generated).  Have Petunia call this instead of running the executable directly to avoid mis-communication to user when no .new file is created (i.e. index was good)
+* ''cramp''
+** use index for speed in reading peakLists
 ** Fixed bad logic (from r6329) that prevented fallback capture of scans and charge from spectrum names
 ** Plug various memory leaks
+** fix bug when processing filtered mzML files
+** Apply -C (correct charge states) automatically for OMSSA files
+** clean up usage statement and enzyme display
 * ''ProteinProphet''
 * ''iProphet''
-**
+** make use of spectrum_label when available
 * ''PTMProphet''
 * ''Mascot2XML''
-**
+** More descriptive warning messages for poorly formatted Mascot results
+** Allow conversion to proceed after reporting the issues
 * ''Petunia''
 **
-* ''InteractParser''
+* ''PeptideProphet''
-** fix bug when processing filtered mzML files
+** tell Mascot user which scores are missing
-** Apply -C (correct charge states) automatically for OMSSA files
+** SpectraST modeling correct errors in initial settings
-** clean up usage statement and enzyme display
 * ''subsetdb''
 * Apache/conf
 **
-* Updated README/build notes
 ** Enable SIMD in tandem code to compile under MINGW gcc
 ** Enable -std=c++11 for sufficiently high versions of gcc
+** compile InteractParser with gsl for stats
+** changes to compile on RedHat OS7 gcc 4.8.2
+** Use std::isnan to allow pwiz to compile, include <cmath>
+** Adding back protovis which is utilized in RTCatalog for drawing RT gradient corrections page
+** Fix problem with windows build not copying the pwiz msi to the staging area
+** Fix runtime bug with using boost regex match extra flag ... was crashing PepXMLViewer
 * ''ProtXMLViewer''

TPP:5.2.0 Release Notes

From SPCTools

Revision as of 00:48, 22 December 2018

Contents

Major Changes

New Features

Improvements/Changes

Bug Fixes

Miscellaneous

Known Issues

Getting the TPP Software

Acknowledgements

SVN Log

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