new TPP release: 4.2 revision 1 (4.2.1)
Natalie Tasman
(TPP) software, 4.2.x series, bringing the current version to 4.2
revision 1 (4.2.1). Releases are
available for native windows as well as linux and Mac OS X 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).
All mzXML converters are, as usual, included with the Windows TPP
installation, and can also be downloaded individually.
This release contains many bugfixes as well as some new features. And
as always, you are invited to post to the spctools-discuss mailing
list with any questions or issues with the TPP software.
Changes in 4.2.1 (see also
http://tools.proteomecenter.org/wiki/index.php?title=4.2.1_Release_Notes)
==mzXML converters==
===all mzXML converters===
*mzXML output: fixed a typo that caused index offset corruption for
>2GB output files
===trapper===
*IMPORTANT: if you have a previously installed version of this
software, uninstall the older version (from the start menu->trapper
uninstaller) BEFORE installing the new version. This will ensure that
the updated MassHunter version 2 API is correctly installed.
*Changes from David Horn, Agilent, to address issues with Agilent
MHDAC in which dual-mode files were always converted in peak-picked
(centroided) mode. Tested by David Horn and beta tested by Agilent
customers.
*removing beta mzXML native scan reference; trouble for some strict
parsers (and will return properly in
mzML output when 1.1 finalized.)
===ReAdW===
*updating filterline to parse enchanced flag "E"; previously
documented as for magnetic sector instruments only, but now reported
from LTQ-FT instruments. NOTE: parsing only, not recording this.
*if scantype "Q1MS" is encountered, set msLevel to 1, as the "MS
order" (ms, ms2, etc) indicator is not always present in filterlines.
===mzWiff===
* disable experimental code which gave a 30% speed increase but had
memory leak issues
* Added "-GC" "guess charge" charge state determination code; attempts
to match the "export to MGF" option in Analyst, with about 85%
agreement. NOTE: still untested with MS/MS averaging option)
==PeptideProphet==
*Important fix for mixture distribution bug for +6 and +7 charge states.
*Added unique peptide ion option for PeptideProphet.
==iProphet==
*Fix page display for iProphet result.
*Added unique peptide sequence option for iProphet
==Tandem2XML==
*when parsing scan info from description, watch for mass spec file
extensions that may be substrings of the actual extension (as in mzXML
vs mzXML.gz)
==ProtXML display==
* Fix broken stylesheet for gaggle namelist.
* HTML optimizations: replace single document-wide table with 1 table
per protein group; replace long links with javascript ones.
Preliminary results: page load times are 35% of original (html only),
file size is reduced by >20%
==Petunia==
*anticipate possible .gz extension to input mz[X]ML filename for x!tandem
*file browser should display .gz version of .mzXML, .pep.xml, etc
==utilities==
*pep_dbcount, subsetdb, digestdb, compareProts.pl are now included in
the installation;
*utils. are updated to build with current version of RAMP
*added translateDNA2AA-FASTA which translates a DNA FASTA file to
protein FASTA file
*digestdb: make sure 1st word of sequence def line is properly
terminated when read in
*calctppstat.pl: changes from PeptideAtlas project include
Output (STDOUT):
- the string "Peptide Count" is replaced with "Peptide Count at
P>0.9" in one line
Summary file:
- the string "FDR at 0.90" replaced by "FDR at P 0.90"
- "Proteins identified" line moved to new ProteinProphet section at end
- "Distinct modified peptides": line no longer printed
- Additional lines regarding fraction semi-tryptics and missed cleavages
- Approximately nine new lines at end describing ProteinProphet results
Option --FDRthresh now calculates as many statistics as possible
with regard to an FDR threshold (default 0.01) instead of a
probability threshold. Recommended.
==misc. from David S==
*Added local FDR 45 degree plot.
*Added uncertainty whiskers.
*Fixed decoy_ratio
==known issues==
*massWolf: charge state information is not recorded in output mzXML
*trapper: some users still report problems with stand-alone installations
*trapper: report of problems with QQQ instruments
*trapper: report of problems with thresholding
Download the TPP version 4.2.1 native windows installer
(TPP_Setup_v4_2_JETSTREAM_rev_1.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_4-2-1
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: Natalie, David, and Luis