My new page

Test of new TPP release notes template

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