TPP:4.2.1 Release Notes
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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
