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	= Known Issues =		= Known Issues =
-	* (none)	+	* There are some issues with PTMProphet in 6.3.0 and 6.3.1. Please upgrade to 6.3.2+ if using this tool.
-		+	* SpectraST crashes in all 6.3.x versions. An update is forthcoming.
-		+
	= Getting the TPP Software =		= Getting the TPP Software =

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Revision as of 17:45, 24 August 2023

Trans-Proteomic Pipeline (TPP) software, release 6.3.0 is a major release of TPP that contains new features, improvements, and fixes to 6.2.0. 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 TPP software"). Most users are recommended to use the Windows installer, which installs and configures TPP and other required software (such as a web server). For advanced users who need to customize 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 6.2.0)

Previous release notes are available at TPP:6.2.0_Release_Notes

Contents 1 Major Changes 2 Analytical Tools 2.1 PeptideProphet 2.2 iProphet 2.3 PTMProphet 2.4 ProteinProphet 2.5 SpectraST 2.6 DISCO 2.7 Libra 2.8 InteractParser 2.9 promast 2.10 decoyFastaGenerator.pl 2.11 comparePeps_Categories.pl 2.12 KDModel 2.13 mzParser 3 Interfaces 3.1 Petunia 3.2 PepXMLViewer 3.3 ProtXMLViewer 3.4 Lorikeet 3.5 xinteract 3.6 fileDownloader 3.7 tpp_files 3.8 XPRESS Peptide 3.9 mzTrace 3.10 TPP Landing page 4 System / Other 5 Known Issues 6 Getting the TPP Software 7 Acknowledgements

Major Changes

⭐ Update to Comet 2023.01.2

Analytical Tools

PeptideProphet

👍 New Features

• New models for MSBooster statistics of delta RT loess and unweighted spectral entropy

✅ Bugfixes

• when reporting ZACCMASS parameters in search_summary make sure each type of model is available

iProphet

✅ Bugfixes

• report heteroxl value as a parameter for xl data when HETEROXL model is enabled
• adjust HETEROXL model so pseudocounts are assigned to positive and negative model based on the updated prior probability of an xl id being correct.

PTMProphet

👍 New Features

• now different neutral losses for different amino acids (same PTM) are now possible to define (e.g. ST:79.966331:-97.976896,HY:79.966331:-79.966331) ptmprophet will collapse these to a single ptm type HYST:79.966331 but use different neutral losses for HY ans ST

✅ Bugfixes

• correct reporting of modified peptides with n-term mods (discovered by Eric)
• fix reporting and updating modification_info in pepXML (discovered by Eric)
• modifications were not being updated to the most likely mod site (reported by Eric)

ProteinProphet

✅ Bugfixes

• Restore reporting of percent_coverage that has been broken since TPP 6.1.0

SpectraST

👍 New Features

• SpectraST update to use Proforma, mzPAF

🚀 Improvements

• Adjustments to peak annotation and shuffle-and-reposition decoy methods
• Set default fragmentation type to HCD (used to be CID, which is now becoming rare)

✅ Bugfixes

• Fix bug of decoy generation from non-mzPAF annotated libraries
• better memory handling for multi threading
• ptms defined using arbitrary/user defined decimal precision in interact style notation e.g. C[160.031] used by PTMProphet for localization of arbitrary massdiffs.
• Adjustment to clustering algorithm for high-res data

DISCO

👍 New Features

• implement unweighted spectral entropy calculation on traces, sort traces by entropy first
• GZIP option to save compress the file

🚀 Improvements

• zero out precursor intensity for 'faked' peaks

Libra

🚀 Improvements

• Never use/quantify a spectrum with zero intensity across ALL channels
• Report peptide ratios to two decimal places instead of three
• Set floor to 1e-3 in order to avoid negative INF when intensities are equal/close to zero [still TBD if this is the most optimal value]
• added TPP version info to tag output

✅ Bugfixes

• report protein ratio in TSV output for protein name in protXML entry (instead of pulling name from pepXML tags)

InteractParser

👍 New Features

• New option to read and record MSBooster statistics of delta RT loess and unweighted spectral entropy from a PIN file produced by MSBooster

✅ Bugfixes

• re-correct issue with terminal mods (found by Eric) that have to be reported in file with multiple msms_run_summary tags
• make sure terminal mods are reported AFTER aminoacid mods per the schema (issue found by Jimmy)
• propagate terminal mods use in the search when processing a file with multiple runs.

promast

🚀 Improvements

• Preserve I/L fidelity of input sequences when reporting mapping results

decoyFastaGenerator.pl

👍 New Features

• new option -o to create one decoy set instead of two independent sets

comparePeps_Categories.pl

🚀 Improvements

• Don't output stats when there are no stats
• scientific notation

KDModel

🚀 Improvements

• when reporting models use 6 significant digits

mzParser

✅ Bugfixes

• fix problem with qsort when the index needs to be sorted, replaced std::sort, which is also faster

Interfaces

Petunia

🚀 Improvements

• Add IBT-10 and -16 reporter masses to Libra conditions page
• Reformat new folder/subdir input and button for a more logical UI flow
• Re-style file upload entry field and New file Cancel button
• Put PTMProphet options before iProphet options
• Flag when %CPU utilized in a node is over 105% of actual CPUs in Cluster page

✅ Bugfixes

• Give meaningful error when no file selected to upload
• Only allow use if user matches remote (sudo) user, on regis
• Fix link to (updated?) .raw metadata file

PepXMLViewer

👍 New Features

• New option to require all protein mappings to match required protein text
  • useful for filtering for decoys when there are multimapping decoys that also map to non-decoys (feature suggested by Seamus)
• Since different neutral losses for different amino acids (same PTM) are now possible to define in PTMProphet (e.g. ST:79.966331:-97.976896,HY:79.966331:-79.966331) PepXMLViewer will collapse these to a single ptm type HYST:79.966331 for display purposes

🚀 Improvements

• adding unweighted_spectral_entropy and delta_RT_loess for display

✅ Bugfixes

• correct filtering for proteins in the case of xl type data from Kojak

ProtXMLViewer

🚀 Improvements

• Replace name of Num_Peptides filter with more apt Num_PSMs; no functionality change

✅ Bugfixes

• Restore command-line functionality
  • for generating full-data TSV files as well as one or two column data

Lorikeet

🚀 Improvements

• Add more immonium ions (provided by Eric D.)

xinteract

👍 New Features

• Have PTMProphetParser run on PeptideProphet results, before iProphet instead of after

fileDownloader

🚀 Improvements

• use https to fetch from PAtlas

✅ Bugfixes

• Bugfix file names with subdirs

tpp_files

🚀 Improvements

• Return a path URL as well as a filesystem path for those applications that need it

XPRESS Peptide

👍 New Features

• Added basic start/end scan curation to Label-Free interface

🚀 Improvements

• Enable "Save" button only after user clicks on "Quantitate"
• Added CID label to plots

✅ Bugfixes

• set scan of peak to zero when no signal is found in scan range

mzTrace

✅ Bugfixes

• v3.3.1 RAWPEAK flag

TPP Landing page

🚀 Improvements

• Update latest TPP publication info

System / Other

• Fix issues with parsing correct precursor ion from higher msLevel (>2) spectra
• Support really, really, really, large file name sizes
• Upgrade wget to GNU Wget 1.21.3-win64 built on msys
• Some memory management and multi-threading improvements
• Silence some compiler warnings

Known Issues

• There are some issues with PTMProphet in 6.3.0 and 6.3.1. Please upgrade to 6.3.2+ if using this tool.
• SpectraST crashes in all 6.3.x versions. An update is forthcoming.

Getting the TPP Software

• Download the TPP version 6.3.0 native windows installer (TPP_Setup_6.3.0.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 6.3.0 source code .tgz package

• Or, check out the code directly from svn:

 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_6-3-0

• 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.