TPP:4.2.0 Release Notes

From SPCTools

To developers: Please add anything you want to be sent out here. I'll take out the author attribution in the actual announcement. We can keep this page (or something similar) on the Wiki, as well.

Contents 1 from Natalie 2 from Brian 3 from David 4 from Luis

from Natalie

• build system:
  • C++ makefile/build: includes are now normalized and relative to src dir.
• pepXMLViewer:
  • now validates as xhtml 1.0
  • compatibality with Google Chrome brower
  • more resilient error handling
  • xpress decimal ratio displayed (sortable)
  • xpress min. area filter
  • SpectraST links fixed
  • filtering on NTT
  • choice of L:H or H:L ratios for both xpress and ASAPRatio
• Windows native installer:
  • SSRCalc env variable is now properly set (and uninstalled)
• schemas:
  • protXML schema updated to revision 6; adds optional calculated neutural peptide mass to indistinguishable peptide element
  • pepXML schema updated to revision 13; adds charge states +6 and +7
• perl
  • modifications for using (optional) non-system perl interpreter

from Brian

• ASAPRatioPeptideParser speed improvement from 10x for small compute-bound files to 300+x for larger disk bound files.
• compressed file I/O:
  • Gzipped (.gz) pepXML, protXML and mzXML or mzML files are now treated as native formats, for reduced disk usage and easier sharing across networks:
  • The various mz(X)ML converters now accept a -g (and --gzip, in many cases) argument to produce .mz(X)ML.gz directly
  • tpp_gui.pl allows users to select gzip output from converters
  • tpp_gui_config.pl allows for making gzipped mzXML/mzML/pepXML/protXML the default
  • You can simply add .gz to your output filename and the pipeline will know to gzip the pepXML and protXML files it produces.

from David

• ASAPRatio:
  • N15 labelling support in ASAPRatio
• InteractParser:
  • minimum peptide length parameters sets is_rejected attribute for peptide entries that are too short
• PeptideProphet:
  • Automatically disable RT model when there is insufficient data or poor correlation.
  • Tuning semi-parametric model to improve modeling performance (and reduce FDR)
  • Extending MAX_CHARGE to 7 (common in ETD data), charge must be known first
  • Auto-detect refinement in XTandem and disable NTT model
  • Use is_rejected attribute in pepXML to invalidate peptides of insufficient length.
  • Allow IUPAC ambiguous amino acid symbol B to be considered valid for a glyco motif.
  • Automatically disable the use_decoy_ flag when no decoys exist with given label
• ProteinProphet:
  • New features: Minimum independence parameter, confidence calculation using States et. al.-like algorithm with a Poisson model and some additional controls to tweak MU ( enabled when PROTLEN option is used) , for IPROPHET print alternative peptide forms as indistinguishable_peptides in the protXML file.
  • Improved viewing of iProphet results now displays alternative peptide version (modifications, charges)
• iProphet:
  • Adding back true-NSE statistic
  • using unified EM approach for all models

from Luis

• Petunia:
  • New iProphet tab, plus support within xinteract
  • Added NOMNC option to xinteract
  • Fix link to Tandem output file when input is mzML
  • Removed a couple of redundant 'use' statements