TPP:4.2.1 Release Notes

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1 mzXML converters
2 PeptideProphet
3 iProphet
4 Tandem2XML
5 ProtXML display
6 Petunia
7 utilities
8 misc. from David S
9 known issues

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mzXML converters

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all mzXML converters

mzXML output: fixed a typo that caused index offset corruption for >2GB output files

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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.)

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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.

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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)

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PeptideProphet

Important fix for mixture distribution bug for +6 and +7 charge states.
Added unique peptide ion option for PeptideProphet.

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iProphet

Fix page display for iProphet result.
Added unique peptide sequence option for iProphet

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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)

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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%

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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

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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.

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