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Test of new TPP release notes template

Contents

TPP 6.2.1 Release Notes

Legend

  • 👍 New Feature
  • 🚀 Improvements
  • ✅ Bugfix


Major Changes

⭐ Update to Comet 2023.01.1


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 3.14.2023) ...


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


DISCO

👍 New Features

  • implement unweighted spectral entropy calculation on traces, sort traces by entropy first


Libra

🚀 Improvements

  • Never use 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 best 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 in sourceforge.net/p/sashimi/code/8577/)
  • 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


Interfaces

Petunia

🚀 Improvements

  • Add IBT-10 and -16 reporter masses to Libra conditions page

✅ Bugfixes

  • 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.cgi 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


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 1.21.2 built on msys
  • Some memory management improvements
  • Silence some compiler warnings
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