TPP:5.2.0 Release Notes

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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


Contents

Major Changes

  • New tpp2mzid, a new tool for converting PepXML and ProtXML to mzIdentML.
    • Includes reference parsing libraries
    • Deprecates mzIMLTools


  • New ProteoMapper tools: clips and promast, for fast and efficient mapping of peptide sequences to a proteome
    • Supports variants via PEFF format
    • Able to do fuzzy matching of sequences, including isobaric (with and without mass modifications)


  • New quantitation tool QUANTIC (quantify via annotated ion current)
    • uses matched ion intensities of identified (MS/MS) spectra


  • New tool to generate quantitative volcano plots on Proteins and Peptides, comparePeps_Categories.pl


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


New Features

  • PeptideProphet
    • support for Magnum and Morpheus search engines
  • Libra
    • Expanded UI support for up to 12 channels
    • Added channel defaults for TMT-11
  • InteractParser
    • Report base peak intensity , 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
    • Added support for new PTMProphet fields: norm_entropy and mean_best_prob
    • Implement background color gradient for intensity-based XPRESS ratios
    • Allow export of PTMProphet features and Quantic results
  • 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")
  • Pep3D
    • Display instrument and ms run info


  • Include comet 2018.01.4 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 v3.0.11841 (3.0.1908 on Windows, which does not require .NET 3.5)
  • Updated to latest version 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
    • Skip PEFF-style comments (which start with "#")
  • ProteoWizard
    • set centroid CV term
  • PTMProphet
    • use ppm fragment tolerance
    • 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
    • switching ROC curve to use MBPr
    • only fit the pos observations and neg observations once when learning the model
    • improve progress report
  • Disco
    • implement support for analysis of simply formated RT mz tables files
    • 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
    • Now using case insensitive matching to compare sample_enzyme to enzymatic_search_constraint enzyme information
  • 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 ability to specify location of ProteoWizard (msconvert) installation via separate (user-settable) variable
    • Added option to run XPRESS label-free analysis
    • Re-arranged XPRESS options for more logical/visual flow
    • Default minProb = 0.0 for xinteract
    • Always show File Output options for xinteract, iProphet, PTMProphet, and ProteinProphet pages
    • Try to get correct .ipro* output filename in PTMProphet form
    • Remove StPeter option for exporting non-normalized results
    • Added Quantic page
    • Centralized PTMProphet options form:
      • Remove neutral loss options
      • remove ms1 ppm tolerance option
      • set default minprob=0.5
      • add drop-down to help choose ms2 ppm tolerance
    • Moved Mayu to External Tools menu
    • Removed page for idConvert (use TPP2MzId)
    • Removed rarely used $doMzXMLGzip (auto select gzip when converting)
    • Removing references to mzXML in favor of mzML
    • Minor changes in menu wording
    • Increased size of text box in msconvert user params, from 50 (max 500) to 90 (900)
  • 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
    • report PTMProphet stats for different mod types in different columns
    • Added more PTMProphet filters
    • Recreate models file if it is older than pepXML file
  • 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
    • Added support for TMT-11 reporter ions
    • Enhancements to precursor peaks and associated neutral losses
    • 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
    • when reading catalog ignore the header line
    • Report RT in minutes
  • RTCalculator
    • function to read coefficients from a user specified file
  • 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
  • Mascot2XML
    • updates to allow handling of newer mascot results
  • SpectraST
    • New function for returning the nearest peak to a given mz value in a spectrum
    • Added library function flexibility and PTMProphet support
  • 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)
  • fetchDataset
    • version 0.8.1: adds support for downloading http/ftp * .gz datasets
  • cramp
    • use index for speed in reading peakLists
  • Install
    • added basic check for required perl modules
    • Configure _PORT_ and tandem_params on Linux installations


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
  • 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
    • address long standing memory issues
  • Mascot2XML
    • More descriptive warning messages for poorly formatted Mascot results
    • Allow conversion to proceed after reporting the issues
  • Petunia
    • Remove unnecessary tags from stylesheet
  • xinteract
    • fix commandline parsing for PTMProphet options that includes "...THREADS=..."
  • DISCO
    • Fix file output of intermediate results on Windows
    • Test for spectrum list bounds overruns as QE DIA data may not have complete cycles
  • batchcoverage
    • Fix memory leaks, clean up code
  • SpectraST
    • Fix MSP import of latest NIST HCD libraries
    • PepXML import allows modification specified as SpectraST-recognized mod names (in place of "mass" in mod_aminoacid_mass). This is a temporary fix until we have better ways of specifying mods in PepXML.
  • 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!)
    • fix memory issue
  • 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
    • ascertain indexes are sorted and the peaks are being read properly using the index
  • Apache/conf
    • Add Apache 2.4 directives for TPP (new file which can be used instead of default for 2.2)


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
    • Build updates for newer compilers. Tested on Mingw64 with gcc 7.3.0 and RedHat 7.4 with gcc 4.8.5.
    • 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
    • add libgd to Linux targets
  • 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

  • MASSDIFFMODE is not working in PTMProphet
  • PepXMLViewer export of Quantic values is broken

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.

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