From SPCTools

Test of new TPP release notes template

Contents 1 TPP 6.2.1 Release Notes 1.1 Major Changes 1.2 Analytical Tools 1.2.1 PeptideProphet 1.2.2 iProphet 1.2.3 PTMProphet 1.2.4 ProteinProphet 1.2.5 SpectraST 1.2.6 DISCO 1.2.7 Libra 1.2.8 InteractParser 1.2.9 promast 1.2.10 decoyFastaGenerator.pl 1.2.11 comparePeps_Categories.pl 1.3 Interfaces 1.3.1 Petunia 1.3.2 PepXMLViewer 1.3.3 ProtXMLViewer 1.3.4 XPRESS Peptide 1.3.5 mzTrace 1.3.6 TPP Landing page 1.4 System / Other

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