TPP:6.2.0 Release Notes

From SPCTools

(Difference between revisions)
Jump to: navigation, search
Revision as of 09:04, 9 January 2023
Luis (Talk | contribs)

← Previous diff		 Revision as of 01:53, 10 January 2023
Luis (Talk | contribs)

Next diff →
Line 9: Line 9:
= Major Changes = = Major Changes =
 +
 +* ''Comet'' version 2022.01.2 (with Makefiles corrected)
 +* ''Kojak'' version 2.0.3 (See kojak-ms.org for complete details)
 +* ''ProteoWizard'' version 3.0.22340 [77d5bfc] (Note updated licenses)
 +* ''calctppstat'' rev 397
 +
 +
= New Features = = New Features =
 +* ''Petunia''
 +** Added pages for ThermoRawFileParser and tdf2mzml (Bruker) mzML converters
 +** Libra conditions page:
 +*** Add pseudo-counts and new maxChannels parameters
 +*** Bump number of Libra channels to 30
 +*** Add input for user-specified file name for Libra TSV output (quantitation.tsv)
 +*** Update TMT-16 isotopic correction coefficients
 +*** Added TMT-18 option
 +** Enable/add threads parameter for:
 +*** iProphet
 +*** xinteract (also passes value to PTMProphet, if running it)
 +*** reSpect
 +*** Quantic
 +*** Disco
 +*** Kojak and Magnum (value is extracted from params file)
 +** AWS cluster page:
 +*** Dynamically select AMI to launch via amztpp based on local TPP version
 +**** makes wget call to get list of AMIs (hosted at ISB)
 +*** Update AMZ AMI for TPP 6.1.x
 +*** Minor layout updates to AMZ cluster page
 +
 +* ''Lorikeet''
 +** Added support for labile mass losses and N-term mod fragmentation
 +** Enable mouse-over highlight of peaks (MS1 and MS2) and massdiff windows
 +** Add mouse-over tooltips to MS1 window
 +** Display m/z values to four decimal places and intensities to two
 +** Update jQuery to 3.5.1 and only inlcude Slider from jQuery-ui (1/3/22)
 +** Add Formyl loss
 +
 +* ''PepXMLViewer''
 +** Display (fake-XTandem) scores as reported by MSFragger
 +** Attempt to find database in same directory as input pepXML file if supplied path is not valid (e.g. not a full path)
 +** Add filtering options for all Libra channels
 +** Add filter by Protein Description (suggested by M.Maes)
 +** Added support for linking to separate MS3 spectra for xlink data. Separate Lorikeet links show up as "[spectA][spectB]" under the "Ions" column.
 +** Added secondary and tertiary sorting (requested by Rob M)
 +*** Place thick border as an extra visual delimiter when doing secondary sorting on peptide sequence (and primary on protein)
 +** Added option to display stripped peptide sequence (no flanking AAs or mods)
 +** Restore command-line functionality and usage statement
 +** When WEBSERVER_TMP is not set write tmp file to same path as input pepXML file, instead of . to avoid permissions issues etc.
 +
 +* ''ProtXMLViewer''
 +** Attempt to find database in same directory as input protXML file if supplied path is not valid (e.g. not a full path); warn user
 +** Add more separation between peptide and protein sorting options
 +
 +* ''PeptideProphet''
 +** make XLSecondScore and XLTopExpect optionally enabled by the user for Kojak 2.0 xl results
 +** BANDWIDTHX= option to set a multiplicative factor on bandwidth for PeptideProphet NONPARAM model...
 +** function to set RT coefficients file for better control of RT modeling.
 +** new option to specify RT models now allow user to specify a trained neural net from RTCalc for theoretical RT
 +
 +* ''DISCO''
 +** NOEXCLUSION to not apply in silico dynamic exclusion to Hardklor features and go after all features detected by Hardklor in each scan
 +** cosine similarity
 +
 +* ''xinteract''
 +** HETEROXL option for Kojak analysis ...
 +** option BWX= for setting BANDWIDTHX= parameter in PeptideProphetParser
 +** new option to set the decoy rate
 +** BUGFIX negative modifications masses specified as part of the MODSTRING were being incorrectly translated to PTMProphetParser options
 +
 +* ''promast''
 +** Preserve I/L of mapped sequences (unless running on pepXML files in order to mimic RefreshParser, in which case all I become L)
 +** Start a thread per 5k sequences (up from 1k) as default
 +** More explicit warning message when original fasta not found to provide sequence context (and disable context output)
 +** Add a simple check to test whether file is actually an index file; exit with error if it is not
 +
 +* ''Unimod Helper''
 +** Pre-check checkbox when there is only one AA/site option
 +** update to latest Unimod definitions
 +
 +* ''MSToolkit''
 +** filter Spectrum by mz range
 +** update instruments
 +** read more types of ion mobility data encodings
 +
 +* ''PTMProphet''
 +** new feature NOSTACK to disallow stacking of PTMs at the same site
 +** MODPREC= option for allowing the user to specify the PTM floating point precision so very near mass PTMs can be distinguished
 +
 +* ''readmzXML''
 +** Add precursor scan number and isolation window info to MS2 header
 +
 +* ''sage2xml''
 +** Initial version of ''Sage'' to pepXML converter
 +
 +* ''iProphet''
 +** new model HETEROXL=val option can be enabled for cross-linked data from Kojak.
 +*** val sets the number of pseudo-counts to add to each bin of the HETEROXL model
 +
 +* ''Libra''
 +** Added new required maxChannels element to <pseudocount> parameter tag
 +*** specifies maximum number of channels with missing values to use when imputing pseudocounts
 +*** exit with error if value is greater than number of channels used
 +*** tag itself still not required
 +** Write pseudocount user options to pep/prot XML files
 +** Enabled the use of the file name specified in <quantitationFile> for TSV output
 +** Remove references to retired targetMs parameter
 +
 +* ''ProphetModels''
 +** option -L to compute FDR plots for cross-linked PSMs from Kojak
 +** options -u -q in combination with -L for counting on the level of unique xl peptide combinations
 +** -n option allows counting on the level of unique peptide ions, and with -L -u -q on the level of unique xl peptide ion combination for decoy-based validation of Kojak results
 +
 +* ''SpectraST''
 +** API option for setting the floating point precision of PTM tokens
 +
 +* ''HardKlor''
 +** implement support for mz_min mz_max as advertised
 +
 +* ''decoyFastaGenerator''
 +** randomly decide if decoy belongs to DECOY0 or DECOY1 set, instead of alternating
 +*** this helps reduce bias due to order of target input sequences in the database (which might not be random)
 +
 +* ''tpp models''
 +** Capture and display new HeteroXL distributions
 +** Minor changes to display format
 +** Add more obvious warning if a model name cannot be extracted
 +
 +* ''tpp2mzid''
 +** Added a new parameter, -d, to specify a decoy prefix string for decoy sequences in the FASTA search database
 +*** The default value is "DECOY", but the parameter is used to specify any prefix for decoy sequences, which will then be flagged as isDecoy="true" in <PeptideEvidence> elements of the resulting mzID files.
 +
 +* ''NeoPepXMLParser''
 +** Added new element <lability> to <ptmprophet_result>. I have no idea what this is because it is not in the PepXML schema.
 +** Also updated some other elements that seem deviant from the schema.
 +
 +
 +
= Improvements/Changes/Bug Fixes = = Improvements/Changes/Bug Fixes =
 +* ''Petunia''
 +** Some TPP menu items have been re-arranged
 +** Set umask for group write permissions when creating a directory
 +** Delete "shell" command files when deleting a session (and also immediately after calling sinfo/squeue)
 +** Update "command still running" text when job status changes
 +** Add Petunia URL to session info
 +** (SLURM) cluster display:
 +*** Move Cluster link to top-level menu bar
 +*** Render cluster info as html tables, adding context colors and usage bars; add update datetime
 +*** Add ability to kill SLURM job
 +*** Check for SLURM job completion via squeue call (instead of scanning for output files)
 +*** Add color background bar to indicate running time of cluster jobs, with visual cues for long-running entries
 +*** Add filterbox to SLURM jobs table, including a "view mine" quick link
 +*** Reverse-sort list to show RUNNING jobs near the top and PENDING ones below
 +*** Do not truncate sinfo fields
 +*** Slight change to snodes State color logic
 +*** Handle "down" node status
 +** Run 'export' commands separately from main command when sending job to regis cluster
 +** indexMzXML also works on mzML files
 +** Removed obsolete utilities to assign and insert charge states into mzXML files (originally for ETD workflows)
 +** New css class to distinguish Cancel buttons from other Action buttons
 +** Minor updates to filterTable in order to allow tables with multiple classes to be filtered
 +
 +* ''ploTPP''
 +** Enable mouse-drag to select (zoom) x-range in Histogram mode
 +
 +* ''Lorikeet''
 +** Bugfix find correct precursor peak when massdiff == zero
 +** Bugfix correctly calculate matched ion current (antic)
 +** Bugfix base mass diff comparisons for displaying losses on absolute value (found by Jimmy)
 +** Fix potential buffer overrun
 +
 +* ''MADCAPS''
 +** Add dedicated input field for database location, with file Browse widget
 +** Break out javascript code to separate file
 +
 +* ''PeptideProphet''
 +** fix issue with FORCEDISTR affecting search engine results of comet, magnum and kojak
 +** allow for ' ' (comet) or '/' (fragger) separators for searching mass_offsets
 +** special conditions for Kojak scores when the xl peptides are subsequences
 +** BUGFIX correct problem when Kojak and experiment_labels are used
 +
 +* ''DISCO''
 +** BUGFIX was preventing tracking of all identified precursors, new features to allow scanning of other charge states, also now combines a user defined target list with hardklor deterimined features
 +** BUGFIX don't analyze spectra at the borders of neighoring thread loads in both thread neighbors (bug discovered by Kristian)
 +** BUGFIX hardklor config that was limiting MS1 feature detection
 +
 +* ''tpp files''
 +** Bug fix: use getDataPath instead of getDataUrl for navigating the file system
 +
 +* ''ProteinProphet''
 +** More informative error message when no data found in input
 +
 +* ''RtExtract'' v5.4.1
 +
 +* ''clips''
 +** Fix regexp to capture optional VariantSimple parameter
 +** Skip protein entries with no sequence (instead of exiting)
 +** Do not report proteins skipped as a result of user exclusion string unless in DEBUG mode
 +
 +* ''PTMProphet''
 +** change message text when similar mass mod token collisions occur
 +** BUGFIX reporting of certain PTMProphet results containing issues in modification_info tags (discovered by Zhi)
 +** correct dead lock (found by Zhi)
 +** correct threading problem under Linux (discovered by A.Zelter)
 +** BUGFIX correct some threading/heap corruption issues exposed occasionally on Windows (reported by Alexey)
 +** plug a memory leak
 +** BUGFIX correct reporting of modified peptides with multiple PTMs of one type.
 +
 +* ''InteractParser''
 +** Do not use value in -a option (data path) to set base_name attribute of search_summary (this breaks links, and is not the intended use of this attribute)
 +** BUGFIX correct issue with signal to noise option -2
 +
 +* ''mzParser''
 +** report error to user when author of an mzML file leaves bugs in their indexes.
 +
 +* ''SpectraSTPeakList''
 +** don't count peaks already found twice
 +
 +* ''ProphetModels''
 +** Warn if input file cannot be updated to add <decoy> tags instead of displaying obscure perl warning
 +** BUGFIX correct broken decoy counting for XL PSMs
 +
 +* ''tpp2mzid''
 +** fixed bug where SpectrumIdentificationItem id numbers were not incrementing properly.
 +** updated the NeoPepXMLParser library to process the <lability> elements that have appeared in pepXML
 +
 +
 +
= Miscellaneous = = Miscellaneous =
 +* correct various compiler bugs and errors
 +* improvements to speed and threading in some tools
 +* Updates to quiet warnings and errors on Perl 5.30. No functional change.
 +
 +
= Known Issues = = Known Issues =

Revision as of 01:53, 10 January 2023

Trans-Proteomic Pipeline (TPP) software, release 6.2.0 is a major release of TPP that contains new features, improvements, and fixes to 6.1.0. 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 (same as for 6.1.0)


Previous release notes are available at TPP:6.1.0_Release_Notes


Contents

Major Changes

  • Comet version 2022.01.2 (with Makefiles corrected)
  • Kojak version 2.0.3 (See kojak-ms.org for complete details)
  • ProteoWizard version 3.0.22340 [77d5bfc] (Note updated licenses)
  • calctppstat rev 397


New Features

  • Petunia
    • Added pages for ThermoRawFileParser and tdf2mzml (Bruker) mzML converters
    • Libra conditions page:
      • Add pseudo-counts and new maxChannels parameters
      • Bump number of Libra channels to 30
      • Add input for user-specified file name for Libra TSV output (quantitation.tsv)
      • Update TMT-16 isotopic correction coefficients
      • Added TMT-18 option
    • Enable/add threads parameter for:
      • iProphet
      • xinteract (also passes value to PTMProphet, if running it)
      • reSpect
      • Quantic
      • Disco
      • Kojak and Magnum (value is extracted from params file)
    • AWS cluster page:
      • Dynamically select AMI to launch via amztpp based on local TPP version
        • makes wget call to get list of AMIs (hosted at ISB)
      • Update AMZ AMI for TPP 6.1.x
      • Minor layout updates to AMZ cluster page
  • Lorikeet
    • Added support for labile mass losses and N-term mod fragmentation
    • Enable mouse-over highlight of peaks (MS1 and MS2) and massdiff windows
    • Add mouse-over tooltips to MS1 window
    • Display m/z values to four decimal places and intensities to two
    • Update jQuery to 3.5.1 and only inlcude Slider from jQuery-ui (1/3/22)
    • Add Formyl loss
  • PepXMLViewer
    • Display (fake-XTandem) scores as reported by MSFragger
    • Attempt to find database in same directory as input pepXML file if supplied path is not valid (e.g. not a full path)
    • Add filtering options for all Libra channels
    • Add filter by Protein Description (suggested by M.Maes)
    • Added support for linking to separate MS3 spectra for xlink data. Separate Lorikeet links show up as "[spectA][spectB]" under the "Ions" column.
    • Added secondary and tertiary sorting (requested by Rob M)
      • Place thick border as an extra visual delimiter when doing secondary sorting on peptide sequence (and primary on protein)
    • Added option to display stripped peptide sequence (no flanking AAs or mods)
    • Restore command-line functionality and usage statement
    • When WEBSERVER_TMP is not set write tmp file to same path as input pepXML file, instead of . to avoid permissions issues etc.
  • ProtXMLViewer
    • Attempt to find database in same directory as input protXML file if supplied path is not valid (e.g. not a full path); warn user
    • Add more separation between peptide and protein sorting options
  • PeptideProphet
    • make XLSecondScore and XLTopExpect optionally enabled by the user for Kojak 2.0 xl results
    • BANDWIDTHX= option to set a multiplicative factor on bandwidth for PeptideProphet NONPARAM model...
    • function to set RT coefficients file for better control of RT modeling.
    • new option to specify RT models now allow user to specify a trained neural net from RTCalc for theoretical RT
  • DISCO
    • NOEXCLUSION to not apply in silico dynamic exclusion to Hardklor features and go after all features detected by Hardklor in each scan
    • cosine similarity
  • xinteract
    • HETEROXL option for Kojak analysis ...
    • option BWX= for setting BANDWIDTHX= parameter in PeptideProphetParser
    • new option to set the decoy rate
    • BUGFIX negative modifications masses specified as part of the MODSTRING were being incorrectly translated to PTMProphetParser options
  • promast
    • Preserve I/L of mapped sequences (unless running on pepXML files in order to mimic RefreshParser, in which case all I become L)
    • Start a thread per 5k sequences (up from 1k) as default
    • More explicit warning message when original fasta not found to provide sequence context (and disable context output)
    • Add a simple check to test whether file is actually an index file; exit with error if it is not
  • Unimod Helper
    • Pre-check checkbox when there is only one AA/site option
    • update to latest Unimod definitions
  • MSToolkit
    • filter Spectrum by mz range
    • update instruments
    • read more types of ion mobility data encodings
  • PTMProphet
    • new feature NOSTACK to disallow stacking of PTMs at the same site
    • MODPREC= option for allowing the user to specify the PTM floating point precision so very near mass PTMs can be distinguished
  • readmzXML
    • Add precursor scan number and isolation window info to MS2 header
  • sage2xml
    • Initial version of Sage to pepXML converter
  • iProphet
    • new model HETEROXL=val option can be enabled for cross-linked data from Kojak.
      • val sets the number of pseudo-counts to add to each bin of the HETEROXL model
  • Libra
    • Added new required maxChannels element to <pseudocount> parameter tag
      • specifies maximum number of channels with missing values to use when imputing pseudocounts
      • exit with error if value is greater than number of channels used
      • tag itself still not required
    • Write pseudocount user options to pep/prot XML files
    • Enabled the use of the file name specified in <quantitationFile> for TSV output
    • Remove references to retired targetMs parameter
  • ProphetModels
    • option -L to compute FDR plots for cross-linked PSMs from Kojak
    • options -u -q in combination with -L for counting on the level of unique xl peptide combinations
    • -n option allows counting on the level of unique peptide ions, and with -L -u -q on the level of unique xl peptide ion combination for decoy-based validation of Kojak results
  • SpectraST
    • API option for setting the floating point precision of PTM tokens
  • HardKlor
    • implement support for mz_min mz_max as advertised
  • decoyFastaGenerator
    • randomly decide if decoy belongs to DECOY0 or DECOY1 set, instead of alternating
      • this helps reduce bias due to order of target input sequences in the database (which might not be random)
  • tpp models
    • Capture and display new HeteroXL distributions
    • Minor changes to display format
    • Add more obvious warning if a model name cannot be extracted
  • tpp2mzid
    • Added a new parameter, -d, to specify a decoy prefix string for decoy sequences in the FASTA search database
      • The default value is "DECOY", but the parameter is used to specify any prefix for decoy sequences, which will then be flagged as isDecoy="true" in <PeptideEvidence> elements of the resulting mzID files.
  • NeoPepXMLParser
    • Added new element <lability> to <ptmprophet_result>. I have no idea what this is because it is not in the PepXML schema.
    • Also updated some other elements that seem deviant from the schema.



Improvements/Changes/Bug Fixes

  • Petunia
    • Some TPP menu items have been re-arranged
    • Set umask for group write permissions when creating a directory
    • Delete "shell" command files when deleting a session (and also immediately after calling sinfo/squeue)
    • Update "command still running" text when job status changes
    • Add Petunia URL to session info
    • (SLURM) cluster display:
      • Move Cluster link to top-level menu bar
      • Render cluster info as html tables, adding context colors and usage bars; add update datetime
      • Add ability to kill SLURM job
      • Check for SLURM job completion via squeue call (instead of scanning for output files)
      • Add color background bar to indicate running time of cluster jobs, with visual cues for long-running entries
      • Add filterbox to SLURM jobs table, including a "view mine" quick link
      • Reverse-sort list to show RUNNING jobs near the top and PENDING ones below
      • Do not truncate sinfo fields
      • Slight change to snodes State color logic
      • Handle "down" node status
    • Run 'export' commands separately from main command when sending job to regis cluster
    • indexMzXML also works on mzML files
    • Removed obsolete utilities to assign and insert charge states into mzXML files (originally for ETD workflows)
    • New css class to distinguish Cancel buttons from other Action buttons
    • Minor updates to filterTable in order to allow tables with multiple classes to be filtered
  • ploTPP
    • Enable mouse-drag to select (zoom) x-range in Histogram mode
  • Lorikeet
    • Bugfix find correct precursor peak when massdiff == zero
    • Bugfix correctly calculate matched ion current (antic)
    • Bugfix base mass diff comparisons for displaying losses on absolute value (found by Jimmy)
    • Fix potential buffer overrun
  • MADCAPS
    • Add dedicated input field for database location, with file Browse widget
    • Break out javascript code to separate file
  • PeptideProphet
    • fix issue with FORCEDISTR affecting search engine results of comet, magnum and kojak
    • allow for ' ' (comet) or '/' (fragger) separators for searching mass_offsets
    • special conditions for Kojak scores when the xl peptides are subsequences
    • BUGFIX correct problem when Kojak and experiment_labels are used
  • DISCO
    • BUGFIX was preventing tracking of all identified precursors, new features to allow scanning of other charge states, also now combines a user defined target list with hardklor deterimined features
    • BUGFIX don't analyze spectra at the borders of neighoring thread loads in both thread neighbors (bug discovered by Kristian)
    • BUGFIX hardklor config that was limiting MS1 feature detection
  • tpp files
    • Bug fix: use getDataPath instead of getDataUrl for navigating the file system
  • ProteinProphet
    • More informative error message when no data found in input
  • RtExtract v5.4.1
  • clips
    • Fix regexp to capture optional VariantSimple parameter
    • Skip protein entries with no sequence (instead of exiting)
    • Do not report proteins skipped as a result of user exclusion string unless in DEBUG mode
  • PTMProphet
    • change message text when similar mass mod token collisions occur
    • BUGFIX reporting of certain PTMProphet results containing issues in modification_info tags (discovered by Zhi)
    • correct dead lock (found by Zhi)
    • correct threading problem under Linux (discovered by A.Zelter)
    • BUGFIX correct some threading/heap corruption issues exposed occasionally on Windows (reported by Alexey)
    • plug a memory leak
    • BUGFIX correct reporting of modified peptides with multiple PTMs of one type.
  • InteractParser
    • Do not use value in -a option (data path) to set base_name attribute of search_summary (this breaks links, and is not the intended use of this attribute)
    • BUGFIX correct issue with signal to noise option -2
  • mzParser
    • report error to user when author of an mzML file leaves bugs in their indexes.
  • SpectraSTPeakList
    • don't count peaks already found twice
  • ProphetModels
    • Warn if input file cannot be updated to add <decoy> tags instead of displaying obscure perl warning
    • BUGFIX correct broken decoy counting for XL PSMs
  • tpp2mzid
    • fixed bug where SpectrumIdentificationItem id numbers were not incrementing properly.
    • updated the NeoPepXMLParser library to process the <lability> elements that have appeared in pepXML



Miscellaneous

  • correct various compiler bugs and errors
  • improvements to speed and threading in some tools
  • Updates to quiet warnings and errors on Perl 5.30. No functional change.


Known Issues

Getting the TPP Software

  • Download the TPP version 6.2.0 native windows installer (TPP_Setup_6.2.0.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 6.2.0 source code .tgz package
  • Or, check out the code directly from svn: 
 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_6-2-0
  • 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.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:6.2.0_Release_Notes"
Personal tools