new TPP release: 4.2 revision 0 (4.2.0)
Natalie Tasman
(TPP) software, release 4.2 revision 0 (4.2.0). Releases are
available for native windows as well as linux/osx source from all the
usual locations (please see below).
Currently, the Agilent MassHunter .d converter, trapper, remains a
separate manual installation (using "trapper_setup.exe" in
C:\Inetpub\tpp-bin) due to special changes in the Agilent API in this
release (please see below).
Please note, the stand-alone converter release will follow (all
converters included are included in the Windows TPP installation).
This release contains many bugfixes as well as new features. Perhaps
the most noticeable changes are a dramatic speed improvement in
ASAPRatio, and the way that protein grouping works in ProteinProphet.
Read more about the 4.2.0 release below.
And as always, you are invited to post to the spctools-discuss mailing
list with any questions or issues with the TPP software.
== Important changes to ProteinProphet behavior ==
Major changes to protein grouping and subsumed protein behavior have
been made, in order to more accurately compute and display these
relationships. Previously, subsumed proteins would appear
independently of their subsuming protein. Now, the subsumed protein
will appear as an entry in a protein group around the parent protein.
The meaning of "protein group" has changed: while there is still a
group probability, there are proteins in the group that could have
independent evidence. Also, many more proteins will appear together
in groups because any network of proteins with shared peptides are now
counted as a "group".
These changes are due to the introduction of the concept of minimum
independence in ProteinProphet. This parameter sets a threshold of the
minimum ratio of independent (default 0) to shared peptides that a
protein (and any protein that shares its peptides) must earn to be
displayed as an independent protein entry in ProteinProphet. In one
possible new scenario: "Two proteins that share a peptide, and yet
have other independent evidence, will not appear in a group together.
However, if a third protein appears with this peptide and no other
independent evidence, they will all be grouped."
== trapper (Agilent MassHunter .d converter) ==
* The converter has been updated to work with MassHunter version 2
format .d input directories
* memory usage has been improved for processing of large input files
(Thanks to all beta testers!)
* PLEASE NOTE: If you have an older version of the trapper program
installed, please manually run the exisiting trapper uninstaller (from
the start menu), as the older Agilent API files must be cleanly
removed before installing the new Agilent files.
== build system (for developers) ==
* C++ makefile/build: includes are now normalized and relative to src dir.
* modifications for using (optional) non-system perl interpreter
== 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
== ASAPRatio ==
* ASAPRatioPeptideParser speed improvement from 10x for small
compute-bound files to 300+x for larger disk bound files.
* N15 labelling support in ASAPRatio
== 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.
== 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 ==
* (see major changes, above)
* 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
== Petunia ==
* New iProphet tab, plus support within xinteract
* Added NOMNC option to xinteract
* Fix link to Tandem output file when input is mzML
== known issues ==
* mzWiff: charge state information is not recorded in output mzXML
* massWolf: charge state information is not recorded in output mzXML
* trapper: if dual-mode file is processed, the resulting file is
possibly always converted as centroid (even if centroid is not
selected.)
Download the TPP version 4.2.0 native windows installer
(TPP_Setup_v4_2_JETSTREAM_rev_0.exe) from the Sashimi SourceForge
project file release page:
http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912
For guides to installing and using our software, please see our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-2-0
Please refer to the readme file in TPP/src as well as the wiki.
Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
The SPC Tools Team: Luis, David, and Natalie
Natalie Tasman
trapper are available on the Sashimi file release page (see previous
post for download info.)
(Again, these converters are included in the TPP Windows installation.)
-Natalie