TPP:6.2.0 Release Notes

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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

1 Major Changes
2 New Features
3 Improvements/Changes/Bug Fixes
4 Miscellaneous
5 Known Issues
6 Getting the TPP Software
7 Acknowledgements

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Major Changes

Comet version 2023.01.0 (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

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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

ploTPP
- New option to overlay UNIMOD masses onto plot
  - useful when looking at massdiff values
  - when number of mods in viewport is below 30, list them in a box with values, links, and descriptions
- Added/clarified data stats for number of datapoints TOTAL, PLOTTED, and SKIPPED
- Honor user x/min-max values instead of snapping to closest datapoint(s)
- Enable mouse-drag to select (zoom) x-range in Histogram mode
- Added Zoom Out button

Lorikeet
- Remove core Phospho neutral loss; instead, activate it whenever a mod of +80 is found in peptide sequence.
- 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
- Accommodate super-wide Libra display - e.g. 18 channels

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
- new VMC model that considers ptm Type to reduce false positives in rare ptm searching and new model for reducing false positives in mass_offset searching

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
- user can now specify a charge window to go after features in other charge states

xinteract
- HETEROXL option for Kojak analysis
- option -KOJAK to enable ROC curve analysis on XL type ids with ProphetModels.pl
- 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
- Added option to suppress usage statement when there is an error

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 features DALTONTOL= and DENOISE to better deal with ion trap low res noisy data (suggested by E. Deutsch)
- 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
- Write masses with higher precision

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
- additional options for ROC curve plotting prompted by the curve being skipped over in its entirety under certain assumptions

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
- Add support for mod-specific VMC models
- 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.

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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
- Add failsafe status check for jobs that never made it on the queue
- Minor updates to filterTable in order to allow tables with multiple classes to be filtered

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
- Added legend to alignment and sequence tabs
- Break out javascript code to separate file

PPSX
- Trim form input values
- BUGFIX Capture error from STDERR

PeptideProphet
- correctly handle position=1 cases assigned to the amino acid rather than the terminus
- reduce the number of extra interations past convergence to 5 to save some time.
- BUGFIX correct bug with not counting the terminal mods correctly in the VMC by type count ...
- 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

mzTrace v3.3.0

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
- change the precision and number notation for better readability
- BUGFIX to address issue with lability computation
- BUGFIX correct an issue with localizing two different PTMs on the same type of amino acid in the same PSM
- BUGFIX for stacking of USMs and PTMProphet ptms reported by Eric specifically on Q[111] mods
- BUGFIX associated with variable mod localization on c-term
- 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
- Add support for "index=NNNN" scan parsing
- report error to user when author of an mzML file leaves bugs in their indexes.

SpectraSTPeakList
- don't count peaks already found twice
- if the peak has zeroed out intensity do not match it

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

[edit]

Miscellaneous

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

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Known Issues

(none)

[edit]

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.

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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"