From SPCTools

Trans-Proteomic Pipeline (TPP) software, release 7.3.0 is a major release of TPP that contains new features, improvements, and fixes to 7.2.0. 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 7.2.0)

Previous release notes are available at TPP:7.2.0_Release_Notes

Contents 1 Major Changes 2 Analytical Tools 2.1 ASAPRatio 2.2 XPressPeptide 2.3 Kojak Magnum StPeter 2.4 pwiz 3 Interfaces 3.1 ShowXIC 3.2 CUVALibRe 3.3 Petunia 3.4 PepXMLViewer 3.5 ProtXMLViewer 3.6 Lorikeet 3.7 ASAP peptide 3.8 tpp models 4 Misc Tools 4.1 qsir 4.2 TPP files 5 System / Other 6 Known Issues 7 Getting the TPP Software 8 Acknowledgements

Major Changes

⭐ Update to Comet 2025.01.1

⭐ Major rewrite and overhaul of ShowXIC, a XIC/TIC viewer (see below for details)

Analytical Tools

ASAPRatio

✅ Bugfixes

• Fix long-dormant memory overflow bug only recently uncovered by new compilers

XPressPeptide

👍 New Features

• New commandline switch -Z to look for a closing tag of </msms_run_summary> instead of the default </msms_pipeline_analysis>
  • For use when splitting files for (faster) parallel analysis. Some code cleanup

Kojak Magnum StPeter

✅ Bugfixes

• Include <cstdint> in non-Win builds to avoid SIZE_MAX not declared error (surfaced in Ub24.04)

pwiz

✅ Bugfixes

• Remove boost lib that crashed under Ubuntu 24.04
• Remove strangely-duplicated Makefile directive

Interfaces

ShowXIC

👍 New Features

• Overhaul to a far clearer, cleaner, and responsive interface, with ability to load files and directly set input parameters
  • "Toolbar" controls
  • Data series can be toggled
  • Custom, formatted tooltips
  • Show simple user guide
  • Add page history with full parameters, and enable back/forward browser button

• Capture/display PSM info, and mark its RT on XIC

• Add ability to overlay PSM info from pepXML file
  • uses qsir to extract RT, scan#, prec m/z, mzdiff and ppm, charge, mod sequence, and probability for PSMs that fall within XIC range
  • displayed as a list on a table, with graphical bars for clarity, and markings on the XIC

• User Feedback
  • Show "ISB spinner" when loading data
  • Alert if no MS1 data in file, or if no file specified
  • Clearer status feedback on page banner
  • Return and display a somewhat useful error message (instead of...nothing) when data cannot be extracted

🚀 Improvements

• Streamline TIC calculation by skipping unnecessary mz sorting
• Add JSON output option to CGI so as to avoid outdated HTML output; functionality via previous links/params unaffected
• Major clean code cleanup

✅ Bugfixes

• Re-implement binary search:
  • correctly finds the closest mz peak
  • actually respects user MAXPPM input
  • simpler code than previous versions

CUVALibRe

🚀 Improvements

• auto-load file specified in URL params (as file=<filepath>)
• add static column headings
• enable data labels, with toggle control
• place chart controls in a toolbar at bottom of plot window (in favor of movable "remote control")
• use local chart.js libraries
• layout adjustments
• remove old clustering functions
• minor improvements for eventual GO integration

✅ Bugfixes

• Remove outdated/duplicated code

Petunia

👍 New Features

• Add full comet params file option
• Add RumAndCoke (generates JSON file for CUVALibRe)
• Add link to CUVALibRe (for *.prot.xml.json files)

🚀 Improvements

• Remove obsolete dta2mzxml from menu (code removal TBD)
• Rebalance main menu items
• Remove NIGMS image and add link to ISB Funding page
• Update link to new XIC viewer

PepXMLViewer

🚀 Improvements

• Add link to new XIC viewer, which now includes the modified peptide sequence, scan# and pepXML filepath

✅ Bugfixes

• Fix expect score filtering when small values previous end up as 0.0000, messing up subsequent page updates
• Changed the integer param values to show as integers instead of decimal numbers

ProtXMLViewer

🚀 Improvements

• Make Windows path comparisons case-insensitive
• Add [ + ] to Legend link for clarity

Lorikeet

👍 New Features

• Add link to online Quetzal spectrum annotation utility

ASAP peptide

🚀 Improvements

• Overlay hit data only from relevant MS run
• highlight same-sequence hits

✅ Bugfixes

• silence compiler warnings

tpp models

🚀 Improvements

• New option -R to stop parsing file after main models and header info have been retrieved; skips individual MS Run info
  • Very useful for HUGE files that take a long time to parse

Misc Tools

qsir

🚀 Improvements

• Require mzML path so as to retrieve hit data that corresponds only to that MS run; add RT to returned data
• Deal with Windows paths (backslashes and case insensitivity)

TPP files

🚀 Improvements

• Replace backslashes in paths with forward ones (Windows)

System / Other

• Add simple Makefile to install tpp-python executables
• Generate two sample comet params files: basic (-p) and full (-q)
• Update to version 1.031.6 (latest) of PSI-MOD.obo
• Improve legibility of several usage statements
• Add Chart.js for interactive charts
• Remove links to ProteoGrapher; consider reinstating when/if it can be made more performant, and with recent GO data
• Remove old/obsolete custom GO definition files of unknown provenance
• Remove deprecated web server conf settings
• Purge old/deprecated/stray code and files, including pre-msconvert mz[X]ML converters
• Add html5 DOCTYPE and link to TPP icon to (most) HTML pages

Known Issues

• None

Getting the TPP Software

• Download the TPP version 7.3.0 native windows installer (TPP_Setup_7.3.0.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 7.3.0 source code .tgz package

• Or, check out the code directly from svn:

 svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_7-3-0

• 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: Luis, 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 p\ rovided feedback and code contributions.