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

  • 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
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